Next Issue
Volume 14, November
Previous Issue
Volume 14, September
 
 

Genes, Volume 14, Issue 10 (October 2023) – 148 articles

Cover Story (view full-size image): The heavy-metal-associated (HMA) proteins are a class of PB1-type ATPases related to the intracellular transport and detoxification of metals. We conducted a comprehensive genome-wide analysis of the HMA family in ten Cucurbitaceae species. We identified 103 Cucurbit HMA proteins with various members, ranging from 8 (Legenaria siceraria) to 14 (Cucurbita pepo) across different species. Finally, nine candidate HMA genes were selected. The expression pattern of the CpeHMA genes showed a distinct pattern of expression in root and shoot tissues, with a remarkable expression of CpeHMA6 and CpeHMA3 genes from the Cu/Ag clade. This study provides insights into the functional analysis of the HMA gene family in the Cucurbitaceae species and lays down the basic knowledge to explore the role and mechanism of the HMA gene family to cope with arsenic stress conditions. View this paper
  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.
Order results
Result details
Section
Select all
Export citation of selected articles as:
23 pages, 8408 KiB  
Article
Characteristics of the Accessible Chromatin Landscape and Transcriptome under Different Temperature Stresses in Bemisia tabaci
by Xiaona Shen, Xiaodi Wang, Nianwan Yang, Fanghao Wan, Zhichuang Lü, Jianying Guo and Wanxue Liu
Genes 2023, 14(10), 1978; https://doi.org/10.3390/genes14101978 - 23 Oct 2023
Cited by 1 | Viewed by 940
Abstract
Bemisia tabaci is an important invasive pest with worldwide distribution and strong temperature tolerance. Previous studies have shown that temperature tolerance varies significantly between the different invasive populations. Several key factors involved in epigenetic regulation have been identified and verified in B. tabaci [...] Read more.
Bemisia tabaci is an important invasive pest with worldwide distribution and strong temperature tolerance. Previous studies have shown that temperature tolerance varies significantly between the different invasive populations. Several key factors involved in epigenetic regulation have been identified and verified in B. tabaci; therefore, epigenetic adaptation mechanisms may also exist. This study aimed to detect changes in the chromatin accessibility landscape and genome-wide transcriptome under different temperature stresses in B. tabaci. Assay for transposase-accessible chromatin with high-throughput sequencing and RNA-seq analyses indicated that transcriptional activity of the genes strongly correlates with chromatin accessibility. Chromatin transcription-activated gene expression regulation is dominant during high-temperature stress in B. tabaci, mainly through the transcriptional repression of genes related to low-temperature stress resistance. Furthermore, B. tabaci resists low-temperature stress by regulating enzyme activities and withstands high-temperature stress by regulating metabolism and synthesis of organic substances, both achieved by altering chromatin accessibility. In summary, this study provides a theoretical basis for exploring changes in gene expression and chromatin accessibility under different temperature stresses, offering a new approach to unravelling regulatory mechanisms underlying the onset of molecular regulation in response to various temperature stress conditions. Full article
(This article belongs to the Section Animal Genetics and Genomics)
Show Figures

Figure 1

13 pages, 2871 KiB  
Article
Impacts of Population Size and Domestication Process on Genetic Diversity and Genetic Load in Genus Ovis
by Dongfeng Wang, Hosein Salehian-Dehkordi, Langda Suo and Fenghua Lv
Genes 2023, 14(10), 1977; https://doi.org/10.3390/genes14101977 - 23 Oct 2023
Viewed by 963
Abstract
In theoretical biology, a prevailing hypothesis posits a profound interconnection between effective population size (Ne), genetic diversity, inbreeding, and genetic load. The domestication and improvement processes are believed to be pivotal in diminishing genetic diversity while elevating levels of inbreeding [...] Read more.
In theoretical biology, a prevailing hypothesis posits a profound interconnection between effective population size (Ne), genetic diversity, inbreeding, and genetic load. The domestication and improvement processes are believed to be pivotal in diminishing genetic diversity while elevating levels of inbreeding and increasing genetic load. In this study, we performed a whole genome analysis to quantity genetic diversity, inbreeding, and genetic load across seven wild Ovis species and five domesticated sheep breeds. Our research demonstrates that the genetic load and diversity of species in the genus Ovis have no discernible impact on recent Ne, and three species within the subgenus Pachyceros tend to carry a higher genetic load and lower genetic diversity patterns. The results coincide with these species’ dramatic decline in population sizes within the subgenus Pachyceros ~80–250 thousand years ago. European mouflon presented with the lowest Ne, lower genetic diversity, and higher individual inbreeding coefficient but a lower genetic load (missense and LoF). This suggests that the small Ne of European mouflon could reduce harmful mutations compared to other species within the genus Ovis. We showed lower genetic diversity in domesticated sheep than in Asiatic mouflon, but counterintuitive patterns of genetic load, i.e., lower weak genetic load (missense mutation) and no significant difference in strong genetic load (LoF mutation) between domestic sheep and Asiatic mouflon. These findings reveal that the “cost of domestication” during domestication and improvement processes reduced genetic diversity and purified weak genetic load more efficiently than wild species. Full article
(This article belongs to the Special Issue Systematic Analysis and Application of Omics Data in Animal Breeding)
Show Figures

Figure 1

13 pages, 996 KiB  
Article
Dynamics of Growth in Purebred Pacu (Piaractus mesopotamicus) and Tambaqui (Colossoma macropomum), and Their Reciprocal Hybrids, under Varied Feeding Programs: Insights from Nonlinear Models
by Woshinghton Rocha Gervaz, Antônio Fernando Leonardo, Diogo Teruo Hashimoto, Ivan Bezerra Allaman, Gabriel Rinaldi Lattanzi and Rafael Vilhena Reis Neto
Genes 2023, 14(10), 1976; https://doi.org/10.3390/genes14101976 - 23 Oct 2023
Viewed by 836
Abstract
We evaluated the growth performance of pacu and tambaqui and their reciprocal hybrids (tambacu and paqui) under different feeding programs. We raised 30 individuals from each species and their respective crosses, distributing them into three replicate cages with 10 individuals each. Throughout the [...] Read more.
We evaluated the growth performance of pacu and tambaqui and their reciprocal hybrids (tambacu and paqui) under different feeding programs. We raised 30 individuals from each species and their respective crosses, distributing them into three replicate cages with 10 individuals each. Throughout the 5-month experimental period, the fish were weighed six times while exposed to diverse feeding regimens involving three commercial diets with varying combinations of crude protein (CP) levels: 24%, 28%, and 32%. Growth curves were adjusted using nonlinear models. The evaluation period was insufficient for adjusting the logistic model for the tambaqui and paqui treatments with the highest initial protein intake. Pure pacu had a higher (p < 0.05) growth rate (k = 0.0185) than in the tambacu hybrid (k = 0.0134) and proved to have an early performance since animals from this group reached their weight at inflection faster. Despite growing more slowly, tambacu reached a higher (p < 0.05) final weight (A = 1137.12) than in the pacu (A = 889.12). Among the feeding programs, animals that received less CP showed greater growth potential; however, longer evaluation is important to verify if the initial CP intake has no significant positive effect on fish growth. Full article
(This article belongs to the Section Animal Genetics and Genomics)
Show Figures

Figure 1

15 pages, 3096 KiB  
Article
Effects of Insulin on Proliferation, Apoptosis, and Ferroptosis in Primordial Germ Cells via PI3K-AKT-mTOR Signaling Pathway
by Liu Ye, Xin Liu, Kai Jin, Yingjie Niu, Qisheng Zuo, Jiuzhou Song, Wei Han, Guohong Chen and Bichun Li
Genes 2023, 14(10), 1975; https://doi.org/10.3390/genes14101975 - 22 Oct 2023
Cited by 1 | Viewed by 1225
Abstract
Primordial germ cells (PGCs) are essential for the genetic modification, resource conservation, and recovery of endangered breeds in chickens and need to remain viable and proliferative in vitro. Therefore, there is an urgent need to elucidate the functions of the influencing factors and [...] Read more.
Primordial germ cells (PGCs) are essential for the genetic modification, resource conservation, and recovery of endangered breeds in chickens and need to remain viable and proliferative in vitro. Therefore, there is an urgent need to elucidate the functions of the influencing factors and their regulatory mechanisms. In this study, PGCs collected from Rugao yellow chicken embryonic eggs at Day 5.5 were cultured in media containing 0, 5, 10, 20, 50, and 100 μg/mL insulin. The results showed that insulin regulates cell proliferation in PGCs in a dose-dependent way, with an optimal dose of 10 μg/mL. Insulin mediates the mRNA expression of cell cycle-, apoptosis-, and ferroptosis-related genes. Insulin at 50 μg/mL and 100 μg/mL slowed down the proliferation with elevated ion content and GSH/oxidized glutathione (GSSG) in PGCs compared to 10 μg/mL. In addition, insulin activates the PI3K/AKT/mTOR pathway dose dependently. Collectively, this study demonstrates that insulin reduces apoptosis and ferroptosis and enhances cell proliferation in a dose-dependent manner via the PI3K-AKT-mTOR signaling pathway in PGCs, providing a new addition to the theory of the regulatory role of the growth and proliferation of PGC in vitro cultures. Full article
(This article belongs to the Special Issue Poultry Genetics and Genomics)
Show Figures

Figure 1

19 pages, 4091 KiB  
Article
Genome-Wide Identification and Expression Analysis of the MADS Gene Family in Tulips (Tulipa gesneriana)
by Jiaojiao Lu, Lianwei Qu, Guimei Xing, Zhenlei Liu, Xiaochun Lu and Xiaori Han
Genes 2023, 14(10), 1974; https://doi.org/10.3390/genes14101974 - 22 Oct 2023
Viewed by 1036
Abstract
To investigate the cold response mechanism and low temperature regulation of flowering in tulips, this study identified 32 MADS-box transcription factor family members in tulips based on full-length transcriptome sequencing, named TgMADS1-TgMADS32. Phylogenetic analysis revealed that these genes can be divided into two [...] Read more.
To investigate the cold response mechanism and low temperature regulation of flowering in tulips, this study identified 32 MADS-box transcription factor family members in tulips based on full-length transcriptome sequencing, named TgMADS1-TgMADS32. Phylogenetic analysis revealed that these genes can be divided into two classes: type I and type II. Structural analysis showed that TgMADS genes from different subfamilies have a similar distribution of conserved motifs. Quantitative real-time PCR results demonstrated that some TgMADS genes (e.g., TgMADS3, TgMADS15, TgMADS16, and TgMADS19) were significantly upregulated in buds and stems under cold conditions, implying their potential involvement in the cold response of tulips. In summary, this study systematically identified MADS family members in tulips and elucidated their evolutionary relationships, gene structures, and cold-responsive expression patterns, laying the foundation for further elucidating the roles of these transcription factors in flowering and the cold adaptability of tulips. Full article
(This article belongs to the Section Plant Genetics and Genomics)
Show Figures

Figure 1

10 pages, 442 KiB  
Article
Sequence Analysis of the Malaysian Low Pathogenic Avian Influenza Virus Strain H5N2 from Duck
by Fatin Ahmad Rizal, Kok Lian Ho, Abdul Rahman Omar, Wen Siang Tan, Abdul Razak Mariatulqabtiah and Munir Iqbal
Genes 2023, 14(10), 1973; https://doi.org/10.3390/genes14101973 - 22 Oct 2023
Viewed by 1464
Abstract
The avian influenza viruses (AIV) of the H5 subtype have the ability to mutate from low pathogenic (LPAI) to highly pathogenic (HPAI), which can cause high mortality in poultry. Little is known about the pathogenic switching apart from the mutations at the haemagglutinin [...] Read more.
The avian influenza viruses (AIV) of the H5 subtype have the ability to mutate from low pathogenic (LPAI) to highly pathogenic (HPAI), which can cause high mortality in poultry. Little is known about the pathogenic switching apart from the mutations at the haemagglutinin cleavage site, which significantly contributes to the virus virulence switching phenomenon. Therefore, this study aimed to compare the molecular markers in the haemagglutinin (HA), neuraminidase (NA), and matrix (M) genes of a locally isolated LPAI AIV strain H5N2 from Malaysia with the reference HPAI strains using bioinformatics approaches, emphasising the pathogenic properties of the viral genes. First, the H5N2 strain A/Duck/Malaysia/8443/2004 was propagated in SPF eggs. The viral presence was verified by haemagglutination assay, RT-PCR, and sequencing. Results showed successful amplifications of HA (1695 bp), NA (1410 bp), and M (1019 bp) genes. The genes were sequenced and the deduced amino acid sequences were analysed computationally using MEGA 11 and NetNGlyc software. Analysis of the HA protein showed the absence of the polybasic cleavage motif, but presence of two amino acid residues that are known to affect pathogenicity. There were also two glycosylation sites (glycosites) compared to the reference HPAI viruses, which had three or more at the HA globular head domain. No NA stalk deletion was detected but the haemadsorbing and active centres of the studied NA protein were relatively similar to the reference HPAI H5N2 isolates of duck but not chicken origins. Six NA glycosites were also identified. Finally, we observed a consistent M1 and M2 amino acid sequences between our LPAI isolate with the other HPAI H5N1 or H5N2 reference proteins. These data demonstrate distinct characteristics of the Malaysian LPAI H5N2, compared to HPAI H5N2 or H5N1 from ducks or chickens, potentially aiding the epidemiological research on genetic dynamics of circulating AIV in poultry. Full article
(This article belongs to the Section Microbial Genetics and Genomics)
Show Figures

Figure 1

15 pages, 3739 KiB  
Article
Characterization and Expression Analysis of Genes from Megalobrama amblycephala Encoding Hemoglobins with Extracellular Microbicidal Activity
by Qijun Wang, Xiaoheng Zhao, Yunlong Liu, Juan Zheng, Hujun Cui, Haotong Wang, Houxu Ding, Hong Liu and Zhujin Ding
Genes 2023, 14(10), 1972; https://doi.org/10.3390/genes14101972 - 22 Oct 2023
Cited by 1 | Viewed by 882
Abstract
Hemoglobin (Hb) usually comprises two α and two β subunits, forming a tetramer responsible for oxygen transportation and storage. Few studies have elucidated fish hemoglobin immune functions. Megalobrama amblycephala is a freshwater-cultured fish prevalent in China. We identified two M. amblycephala hemoglobin subunits [...] Read more.
Hemoglobin (Hb) usually comprises two α and two β subunits, forming a tetramer responsible for oxygen transportation and storage. Few studies have elucidated fish hemoglobin immune functions. Megalobrama amblycephala is a freshwater-cultured fish prevalent in China. We identified two M. amblycephala hemoglobin subunits and analyzed their expression patterns and antibacterial activities. The respective full-length cDNA sequences of the M. amblycephala Hb α (MaHbα) and β (MaHbβ) subunits were 588 and 603 bp, encoding 143 and 148 amino acids. MaHbα and MaHbβ were highly homologous to hemoglobins from other fish, displaying typical globin-like domains, most heme-binding sites, and tetramer interface regions highly conserved in teleosts. In phylogenetic analyses, the hemoglobin genes from M. amblycephala and other cypriniformes clustered into one branch, and those from other fishes and mammals clustered into other branches, revealing fish hemoglobin conservation. These M. amblycephala Hb subunits exhibit different expression patterns in various tissues and during development. MaHbα is mainly expressed in the blood and brain, while MaHbβ gene expression is highest in the muscle. MaHbα expression was detectable and abundant post-fertilization, with levels fluctuating during the developmental stages. MaHbβ expression began at 3 dph and gradually increased. Expression of both M. amblycephala Hb subunits was down-regulated in most examined tissues and time points post-Aeromonas hydrophila infection, which might be due to red blood cell (RBC) and hematopoietic organ damage. Synthetic MaHbα and MaHbβ peptides showed excellent antimicrobial activities, which could inhibit survival and growth in five aquatic pathogens. Two M. amblycephala hemoglobin subunits were identified, and their expression patterns and antibacterial activities were analyzed, thereby providing a basis for the understanding of evolution and functions of fish hemoglobins. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science)
Show Figures

Figure 1

11 pages, 3010 KiB  
Article
Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica
by Meixia Wang, Lei Huang, Yixuan Kou, Danqi Li, Wan Hu, Dengmei Fan, Shanmei Cheng, Yi Yang and Zhiyong Zhang
Genes 2023, 14(10), 1971; https://doi.org/10.3390/genes14101971 - 21 Oct 2023
Viewed by 992
Abstract
Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes [...] Read more.
Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world’s most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica. Full article
(This article belongs to the Special Issue Molecular Phylogenetics and Phylogeography of Seed Plants)
Show Figures

Figure 1

18 pages, 6831 KiB  
Article
Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea
by Zhen Li, Tian Wang, Lan Yun, Xiaomin Ren, Yong Wang and Fengling Shi
Genes 2023, 14(10), 1970; https://doi.org/10.3390/genes14101970 - 21 Oct 2023
Viewed by 973
Abstract
Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation [...] Read more.
Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon’s information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker–trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm. Full article
(This article belongs to the Special Issue Genetic Research and Plant Breeding 2.0)
Show Figures

Figure 1

11 pages, 1518 KiB  
Article
The Draft Genome of the “Golden Tide” Seaweed, Sargassum horneri: Characterization and Comparative Analysis
by Shengqin Wang and Mingjiang Wu
Genes 2023, 14(10), 1969; https://doi.org/10.3390/genes14101969 - 21 Oct 2023
Viewed by 1072
Abstract
Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive “golden tide”, causing [...] Read more.
Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive “golden tide”, causing severe damage to the local economy and coastal ecosystems. In this study, we carried out de novo whole-genome sequencing of S. horneri using next-generation sequencing to unravel the genetic information of this alga. By utilizing a reference-guided de novo assembly pipeline with a closely related species, we successfully established a final assembled genome with a total length of 385 Mb. Repetitive sequences made up approximately 30.6% of this genome. Among the identified putative genes, around 87.03% showed homology with entries in the NCBI non-redundant protein database, with Ectocarpus siliculosus being the most closely related species for approximately one-third of these genes. One gene encoding an alkaline phosphatase family protein was found to exhibit positive selection, which could give a clue for the formation of S. horneri golden tides. Additionally, we characterized putative genes involved in fucoidan biosynthesis metabolism, a significant pathway in S. horneri. This study represents the first genome-wide characterization of a S. horneri species, providing crucial insights for future investigations, such as ecological genomic analyses. Full article
(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)
Show Figures

Figure 1

11 pages, 670 KiB  
Article
Complementary Gene Therapy after Revascularization with the Saphenous Vein in Diabetic Foot Syndrome
by Diana Kupczyńska, Paweł Lubieniecki, Maciej Antkiewicz, Jan Barć, Katarzyna Frączkowska-Sioma, Tomasz Dawiskiba, Tadeusz Dorobisz, Małgorzata Małodobra-Mazur, Dagmara Baczyńska, Konrad Pańczak, Wojciech Witkiewicz, Dariusz Janczak, Jan Paweł Skóra and Piotr Barć
Genes 2023, 14(10), 1968; https://doi.org/10.3390/genes14101968 - 20 Oct 2023
Viewed by 1268
Abstract
Diabetic foot syndrome (DFS) is one of the most serious macroangiopathic complications of diabetes. The primary treatment option is revascularization, but complementary therapies are still being sought. The study group consisted of 18 patients diagnosed with ischemic ulcerative and necrotic lesions in DFS. [...] Read more.
Diabetic foot syndrome (DFS) is one of the most serious macroangiopathic complications of diabetes. The primary treatment option is revascularization, but complementary therapies are still being sought. The study group consisted of 18 patients diagnosed with ischemic ulcerative and necrotic lesions in DFS. Patients underwent revascularization procedures and, due to unsatisfactory healing of the lesions, were randomly allocated to two groups: a group in which bicistronic VEGF165/HGF plasmid was administered and a control group in which saline placebo was administered. Before gene therapy administration and after 7, 30, 90, and 180 days, color duplex ultrasonography (CDU) was performed, the ankle-brachial index (ABI) and transcutaneous oxygen pressure (TcPO2) were measured, and DFS changes were described and documented photographically. In the gene therapy group, four out of eight patients (50%) healed their DFS lesions before 12 weeks. During this time, the ABI increased by an average of 0.25 and TcPO2 by 30.4 mmHg. In the control group, healing of the lesions by week 12 occurred in six out of nine patients (66.67%), and the ABI increased by an average of 0.14 and TcPO2 by 27.1 mmHg. One major amputation occurred in each group. Gene therapy may be an attractive option for complementary treatment in DFS. Full article
(This article belongs to the Special Issue Omics Studies of Type 2 Diabetes and Diabetes-Related Complications)
Show Figures

Figure 1

11 pages, 257 KiB  
Article
Determination of Carrier Frequency of Actionable Pathogenic Variants in Autosomal Recessive Genetic Diseases in the Turkish Cypriot Population
by Aziz Suat Gunsel, Mahmut Cerkez Ergoren, Hatice Kemal, Haniyeh Rahbar Kafshboran, Levent Cerit, Ayla Turgay and Hamza Duygu
Genes 2023, 14(10), 1967; https://doi.org/10.3390/genes14101967 - 20 Oct 2023
Viewed by 1246
Abstract
Whole-exome DNA sequencing is a rich source of clinically useful information for specialists, patients, and their families, as well as elucidating the genetic basis of monogenic and complex diseases in clinical diagnosis. However, interpreting and reporting variants encompassing exome and genome sequence analysis [...] Read more.
Whole-exome DNA sequencing is a rich source of clinically useful information for specialists, patients, and their families, as well as elucidating the genetic basis of monogenic and complex diseases in clinical diagnosis. However, interpreting and reporting variants encompassing exome and genome sequence analysis outcome data are one of the greatest challenges of the genomic era. In this study, we aimed to investigate the frequency and allele frequency spectrum of single nucleotide variants accepted as recessive disease carrier status in Turkish Cypriot exomes. The same sequencing platform and data processing line were used for the analysis of data from 100 Turkish Cypriot whole-exome sequence analysis. Identified variants were classified according to ACMG guidelines, and pathogenic variants were confirmed in other databases such as ClinVar, HGMD, Varsome, etc. Pathogenic variants were detected in 68 genes out of 100 whole-exome sequence data. The carriage rate was the highest in the CYP21A2 gene, causing 21-hydroxylase deficiency (14.70%), 11.76% in the HBB gene causing β-thalassemia, 10.29% in the BTD gene causing biotinidase deficiency, 8.82% in the CFTR gene causing cystic fibrosis, 8.82% in the RBM8A gene causing thrombocytopenia-absent radius syndrome, which is an ultra-rare disease, and 5.88% in the GAA gene causing glycogen storage disease II. The carriage of pathogenic variants in other genes causing the disease (GJB2, PAH, GALC, CYP11B2, COL4A3, HBA1, etc.) was determined as less than 5.00%. Also, the identified variations in the mentioned gene within the examined population were reported. The most prevalent mutation in North Cyprus was a missense variant (c.1360 C>T, p.Pro454Ser) detected in the CYP21A2 gene (rs6445), and the most frequently seen variant in the HBB gene was c.93-21G>A (rs35004220). We investigated reported pathogenic variants by estimating the lower and upper limits of carrier and population frequencies for autosomal recessive diseases, for which exome sequencing may reveal additional medically relevant information. Determining the lower and upper limits of these frequencies will shed light on preventive medicine practices and governmental actions. Full article
(This article belongs to the Section Genetic Diagnosis)
21 pages, 789 KiB  
Review
Lung Inflammatory Genes in Cystic Fibrosis and Their Relevance to Cystic Fibrosis Transmembrane Conductance Regulator Modulator Therapies
by Annalucia Carbone, Pamela Vitullo, Sante Di Gioia and Massimo Conese
Genes 2023, 14(10), 1966; https://doi.org/10.3390/genes14101966 - 20 Oct 2023
Cited by 1 | Viewed by 1235
Abstract
Cystic fibrosis (CF) is a monogenic syndrome determined by over 2000 mutations in the CF Transmembrane Conductance Regulator (CFTR) gene harbored on chromosome 7. In people with CF (PWCF), lung disease is the major determinant of morbidity and mortality and is [...] Read more.
Cystic fibrosis (CF) is a monogenic syndrome determined by over 2000 mutations in the CF Transmembrane Conductance Regulator (CFTR) gene harbored on chromosome 7. In people with CF (PWCF), lung disease is the major determinant of morbidity and mortality and is characterized by a clinical phenotype which differs in the presence of equal mutational assets, indicating that genetic and environmental modifiers play an important role in this variability. Airway inflammation determines the pathophysiology of CF lung disease (CFLD) both at its onset and progression. In this narrative review, we aim to depict the inflammatory process in CF lung, with a particular emphasis on those genetic polymorphisms that could modify the clinical outcome of the respiratory disease in PWCF. The natural history of CF has been changed since the introduction of CFTR modulator therapies in the clinical arena. However, also in this case, there is a patient-to-patient variable response. We provide an overview on inflammatory/immunity gene variants that affect CFLD severity and an appraisal of the effects of CFTR modulator therapies on the inflammatory process in lung disease and how this knowledge may advance the optimization of the management of PWCF. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
Show Figures

Figure 1

15 pages, 7236 KiB  
Article
Seven Additional Patients with SOX17 Related Pulmonary Arterial Hypertension and Review of the Literature
by Natalia Gallego-Zazo, Lucía Miranda-Alcaraz, Alejandro Cruz-Utrilla, María Jesús del Cerro Marín, María Álvarez-Fuente, María del Mar Rodríguez Vázquez del Rey, Inmaculada Guillén Rodríguez, Victor Manuel Becerra-Munoz, Amparo Moya-Bonora, Nuria Ochoa Parra, Alejandro Parra, Patricia Pascual, Mario Cazalla, Cristina Silván, Pedro Arias, Diana Valverde, Vinicio de Jesús-Pérez, Pablo Lapunzina, Pilar Escribano-Subías and Jair Tenorio-Castano
Genes 2023, 14(10), 1965; https://doi.org/10.3390/genes14101965 - 20 Oct 2023
Viewed by 1400
Abstract
Pulmonary arterial hypertension (PAH) is an infrequent disorder characterized by high blood pressure in the pulmonary arteries. It may lead to premature death or the requirement for lung and/or heart transplantation. Genetics plays an important and increasing role in the diagnosis of PAH. [...] Read more.
Pulmonary arterial hypertension (PAH) is an infrequent disorder characterized by high blood pressure in the pulmonary arteries. It may lead to premature death or the requirement for lung and/or heart transplantation. Genetics plays an important and increasing role in the diagnosis of PAH. Here, we report seven additional patients with variants in SOX17 and a review of sixty previously described patients in the literature. Patients described in this study suffered with additional conditions including large septal defects, as described by other groups. Collectively, sixty-seven PAH patients have been reported so far with variants in SOX17, including missense and loss-of-function (LoF) variants. The majority of the loss-of-function variants found in SOX17 were detected in the last exon of the gene. Meanwhile, most missense variants were located within exon one, suggesting a probable tolerated change at the amino terminal part of the protein. In addition, we reported two idiopathic PAH patients presenting with the same variant previously detected in five patients by other studies, suggesting a possible hot spot. Research conducted on PAH associated with congenital heart disease (CHD) indicated that variants in SOX17 might be particularly prevalent in this subgroup, as two out of our seven additional patients presented with CHD. Further research is still necessary to clarify the precise association between the biological pathway of SOX17 and the development of PAH. Full article
(This article belongs to the Special Issue Genetics and Genomics of Rare Disorders)
Show Figures

Figure 1

19 pages, 5219 KiB  
Article
Notch Signaling Regulates Mouse Perivascular Adipose Tissue Function via Mitochondrial Pathways
by Chenhao Yang, Xuehui Yang, Anne Harrington, Christian Potts, Abigail Kaija, Larisa Ryzhova and Lucy Liaw
Genes 2023, 14(10), 1964; https://doi.org/10.3390/genes14101964 - 20 Oct 2023
Cited by 1 | Viewed by 1268
Abstract
Perivascular adipose tissue (PVAT) regulates vascular function by secreting vasoactive substances. In mice, Notch signaling is activated in the PVAT during diet-induced obesity, and leads to the loss of the thermogenic phenotype and adipocyte whitening due to increased lipid accumulation. We used the [...] Read more.
Perivascular adipose tissue (PVAT) regulates vascular function by secreting vasoactive substances. In mice, Notch signaling is activated in the PVAT during diet-induced obesity, and leads to the loss of the thermogenic phenotype and adipocyte whitening due to increased lipid accumulation. We used the Adiponectin-Cre (Adipoq-Cre) strain to activate a ligand-independent Notch1 intracellular domain transgene (N1ICD) to drive constitutive Notch signaling in the adipose tissues (N1ICD;Adipoq-Cre). We previously found that constitutive activation of Notch1 signaling in the PVAT phenocopied the effects of diet-induced obesity. To understand the downstream pathways activated by Notch signaling, we performed a proteomic analysis of the PVAT from control versus N1ICD;Adipoq-Cre mice. This comparison identified prominent changes in the protein signatures related to metabolism, adipocyte homeostasis, mitochondrial function, and ferroptosis. PVAT-derived stromal vascular fraction cells were derived from our mouse strains to study the cellular and molecular phenotypes during adipogenic induction. We found that cells with activated Notch signaling displayed decreased mitochondrial respiration despite similar levels of adipogenesis and mitochondrial number. We observed variable regulation of the proteins related to mitochondrial dynamics and ferroptosis, including PHB3, PINK1, pDRP1, and the phospholipid hydroperoxidase GPX4. Mitochondria regulate some forms of ferroptosis, which is a regulated process of cell death driven by lipid peroxidation. Accordingly, we found that Notch activation promoted lipid peroxidation and ferroptosis in PVAT-derived adipocytes. Because the PVAT phenotype is a regulator of vascular reactivity, we tested the effect of Notch activation in PVAT on vasoreactivity using wire myography. The aortae from the N1ICD;Adipoq-Cre mice had increased vasocontraction and decreased vasorelaxation in a PVAT-dependent and age-dependent manner. Our data provide support for the novel concept that increased Notch signaling in the adipose tissue leads to PVAT whitening, impaired mitochondrial function, increased ferroptosis, and loss of a protective vasodilatory signal. Our study advances our understanding of how Notch signaling in adipocytes affects mitochondrial dynamics, which impacts vascular physiology. Full article
(This article belongs to the Special Issue Cellular and Developmental Biology of Lipid Metabolism)
Show Figures

Figure 1

13 pages, 1517 KiB  
Article
Tissue Circular RNA_0004018 and 0003570 as Novel Prognostic Biomarkers for Hepatitis B-Related Hepatocellular Carcinoma
by Min-Kyu Kang, Gyeonghwa Kim, Jung Gil Park, Se Young Jang, Hye Won Lee, Won Young Tak, Young Oh Kweon, Soo Young Park, Yu Rim Lee and Keun Hur
Genes 2023, 14(10), 1963; https://doi.org/10.3390/genes14101963 - 20 Oct 2023
Cited by 1 | Viewed by 978
Abstract
The clinical significance of hsa_circ_0004018 and hsa_circ_0003570 in patients with hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) is unclear. We aimed to explore the clinical significance and prognostic utility of these two circular RNAs (circRNAs) in patients with HBV-HCC. Based on 86 paired tissue [...] Read more.
The clinical significance of hsa_circ_0004018 and hsa_circ_0003570 in patients with hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) is unclear. We aimed to explore the clinical significance and prognostic utility of these two circular RNAs (circRNAs) in patients with HBV-HCC. Based on 86 paired tissue samples of HCC and adjacent non-HCC, the relative expression profiles of hsa_circ_0004018 and hsa_circ_0003570 were determined using quantitative real-time polymerase chain reactions. The cut-off values were the median expression of each of the two circRNAs in 86 patients with HBV-HCC. The combination group comprised patients with high levels of the two circRNAs. Clinicopathological features, body composition profiles at the L3 level, and survival rates were investigated. The expression of hsa_circ_0004018 and hsa_circ_0003570 was downregulated in HCC tissues compared with non-HCC tissues. High expression levels of hsa_circ_0003570 (hazard ratio (HR), 0.437; p = 0.009) and hsa_circ_0004018 (HR, 0.435; p = 0.005) were inversely independent risk factors for overall and progression-free survival in patients with HBV-HCC, whereas the combination group was also an inversely independent risk factor for overall (HR, 0.399; p = 0.005) and progression-free survival (HR, 0.422; p = 0.003) in patients with HBV-HCC. The combination of hsa_circ_0003570 and hsa_circ_0004018 may be a potential prognostic biomarker for HBV-HCC. Full article
(This article belongs to the Special Issue Non-coding RNAs in Human Health and Disease)
Show Figures

Figure 1

13 pages, 1312 KiB  
Article
Multi-Trait Exome-Wide Association Study of Back Pain-Related Phenotypes
by Irina V. Zorkoltseva, Elizaveta E. Elgaeva, Nadezhda M. Belonogova, Anatoliy V. Kirichenko, Gulnara R. Svishcheva, Maxim B. Freidin, Frances M. K. Williams, Pradeep Suri, Yakov A. Tsepilov and Tatiana I. Axenovich
Genes 2023, 14(10), 1962; https://doi.org/10.3390/genes14101962 - 19 Oct 2023
Viewed by 1158
Abstract
Back pain (BP) is a major contributor to disability worldwide, with heritability estimated at 40–60%. However, less than half of the heritability is explained by common genetic variants identified by genome-wide association studies. More powerful methods and rare and ultra-rare variant analysis may [...] Read more.
Back pain (BP) is a major contributor to disability worldwide, with heritability estimated at 40–60%. However, less than half of the heritability is explained by common genetic variants identified by genome-wide association studies. More powerful methods and rare and ultra-rare variant analysis may offer additional insight. This study utilized exome sequencing data from the UK Biobank to perform a multi-trait gene-based association analysis of three BP-related phenotypes: chronic back pain, dorsalgia, and intervertebral disc disorder. We identified the SLC13A1 gene as a contributor to chronic back pain via loss-of-function (LoF) and missense variants. This gene has been previously detected in two studies. A multi-trait approach uncovered the novel FSCN3 gene and its impact on back pain through LoF variants. This gene deserves attention because it is only the second gene shown to have an effect on back pain due to LoF variants and represents a promising drug target for back pain therapy. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
Show Figures

Figure 1

17 pages, 7345 KiB  
Article
Systematic Pan-Cancer Analysis Reveals X-C Motif Chemokine Receptor 1 as a Prognostic and Immunological Biomarker
by Likun Cui, Liye Zhu, Jie Chen, Chunzhen Li, Yizhi Yu and Sheng Xu
Genes 2023, 14(10), 1961; https://doi.org/10.3390/genes14101961 - 19 Oct 2023
Viewed by 1422
Abstract
Chemokines and their receptors play an important role in immune monitoring and immune defense during tumor growth and metastasis. However, their prognostic roles in pan-cancer have not been elucidated. In this work, we screened all chemokine receptors in pan-cancer and discovered X-C Motif [...] Read more.
Chemokines and their receptors play an important role in immune monitoring and immune defense during tumor growth and metastasis. However, their prognostic roles in pan-cancer have not been elucidated. In this work, we screened all chemokine receptors in pan-cancer and discovered X-C Motif Chemokine Receptor 1 (XCR1) as a reliable immunological and prognostic biomarker in pan-cancer using bioinformation. The TCGA database served as the foundation for the primary research database analysis in this work. XCR1 was downregulated in tumors. Patients with reduced XCR1 showed worse prognoses and a concomitant decrease in immune cell infiltration (DCs and CD8+ T cells). According to a gene enrichment study, XCR1 enhanced immune system performance by promoting T-cell infiltration through the C-X-C Motif Chemokine Ligand 9 (CXCL9)- C-X-C Motif Chemokine Receptor 3 (CXCR3) axis. In addition, XCR1 is mainly expressed in infiltrated DCs and some malignant cells in tumor tissues. Our data revealed the important role of XCR1 in remodeling the tumor microenvironment and predicting the survival prognosis, which could also be used as a sensitive biomarker for tumor immunotherapy. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
Show Figures

Graphical abstract

12 pages, 2900 KiB  
Article
Genome-Wide Association Study of the Reproductive Traits of the Dazu Black Goat (Capra hircus) Using Whole-Genome Resequencing
by Xingqiang Fang, Bowen Gu, Meixi Chen, Ruifan Sun, Jipan Zhang, Le Zhao and Yongju Zhao
Genes 2023, 14(10), 1960; https://doi.org/10.3390/genes14101960 - 19 Oct 2023
Viewed by 1375
Abstract
Reproductive traits are the basic economic traits of goats and important indicators in goat breeding. In this study, Dazu black goats (DBGs; n = 150), an important Chinese local goat breed with excellent reproductive performance, were used to screen for important variation loci [...] Read more.
Reproductive traits are the basic economic traits of goats and important indicators in goat breeding. In this study, Dazu black goats (DBGs; n = 150), an important Chinese local goat breed with excellent reproductive performance, were used to screen for important variation loci and genes of reproductive traits. Through genome-wide association studies (GWAS), 18 SNPs were found to be associated with kidding traits (average litter size, average litter size in the first three parity, and average litter size in the first six parity), and 10 SNPs were associated with udder traits (udder depth, teat diameter, teat length, and supernumerary teat). After gene annotation of the associated SNPs and in combination with relevant references, the candidate genes, namely ATP1A1, LRRC4C, SPCS2, XRRA1, CELF4, NTM, TMEM45B, ATE1, and FGFR2, were associated with udder traits, while the ENSCHIG00000017110, SLC9A8, GLRB, GRIA2, GASK1B, and ENSCHIG00000026285 genes were associated with litter size. These SNPs and candidate genes can provide useful biological information for improvement of the reproductive traits of goats. Full article
(This article belongs to the Special Issue Livestock Genomics, Genetics and Breeding)
Show Figures

Figure 1

14 pages, 3564 KiB  
Article
Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species
by Ru Yi, Wenquan Bao, Dun Ao, Yu-e Bai, Lin Wang and Ta-na Wuyun
Genes 2023, 14(10), 1959; https://doi.org/10.3390/genes14101959 - 18 Oct 2023
Viewed by 903
Abstract
The production and quality of apricots in China is currently limited by the availability of germplasm resource characterizations, including identification at the species and cultivar level. To help address this issue, the complete chloroplast genomes of Prunus armeniaca L., P. sibirica L. and [...] Read more.
The production and quality of apricots in China is currently limited by the availability of germplasm resource characterizations, including identification at the species and cultivar level. To help address this issue, the complete chloroplast genomes of Prunus armeniaca L., P. sibirica L. and kernel consumption apricot were sequenced, characterized, and phylogenetically analyzed. The three chloroplast (cp) genomes ranged from 157,951 to 158,224 bp, and 131 genes were identified, including 86 protein-coding genes, 37 rRNAs, and 8 tRNAs. The GC content ranged from 36.70% to 36.75%. Of the 170 repetitive sequences detected, 42 were shared by all three species, and 53–57 simple sequence repeats were detected with AT base preferences. Comparative genomic analysis revealed high similarity in overall structure and gene content as well as seven variation hotspot regions, including psbA-trnK-UUU, rpoC1-rpoB, rpl32-trnL-UAG, trnK-rps16, ndhG-ndhI, ccsA-ndhD, and ndhF-trnL. Phylogenetic analysis showed that the three apricot species clustered into one group, and the genetic relationship between P. armeniaca and kernel consumption apricot was the closest. The results of this study provide a theoretical basis for further research on the genetic diversity of apricots and the development and utilization of molecular markers for the genetic engineering and breeding of apricots. Full article
(This article belongs to the Special Issue Comparative Genomics and Phylogenetic Relationships among Solanaceae)
Show Figures

Figure 1

8 pages, 707 KiB  
Case Report
Identification of a Novel FOXP1 Variant in a Patient with Hypotonia, Intellectual Disability, and Severe Speech Impairment
by Mario Benvenuto, Pietro Palumbo, Ester Di Muro, Concetta Simona Perrotta, Tommaso Mazza, Giuseppa Maria Luana Mandarà, Orazio Palumbo and Massimo Carella
Genes 2023, 14(10), 1958; https://doi.org/10.3390/genes14101958 - 18 Oct 2023
Cited by 1 | Viewed by 992
Abstract
The FOXP subfamily includes four different transcription factors: FOXP1, FOXP2, FOXP3, and FOXP4, all with important roles in regulating gene expression from early development through adulthood. Haploinsufficiency of FOXP1, due to deleterious variants (point mutations, copy number variants) disrupting the gene, leads [...] Read more.
The FOXP subfamily includes four different transcription factors: FOXP1, FOXP2, FOXP3, and FOXP4, all with important roles in regulating gene expression from early development through adulthood. Haploinsufficiency of FOXP1, due to deleterious variants (point mutations, copy number variants) disrupting the gene, leads to an emerging disorder known as “FOXP1 syndrome”, mainly characterized by intellectual disability, language impairment, dysmorphic features, and multiple congenital abnormalities with or without autistic features in some affected individuals (MIM 613670). Here we describe a 10-year-old female patient, born to unrelated parents, showing hypotonia, intellectual disability, and severe language delay. Targeted resequencing analysis allowed us to identify a heterozygous de novo FOXP1 variant c.1030C>T, p.(Gln344Ter) classified as likely pathogenetic according to the American College of Medical Genetics and Genomics guidelines. To the best of our knowledge, our patient is the first to date to report carrying this stop mutation, which is, for this reason, useful for broadening the molecular spectrum of FOXP1 clinically relevant variants. In addition, our results highlight the utility of next-generation sequencing in establishing an etiological basis for heterogeneous conditions such as neurodevelopmental disorders and providing additional insight into the phenotypic features of FOXP1-related syndrome. Full article
(This article belongs to the Special Issue Molecular Basis and Genetics of Intellectual Disability)
Show Figures

Figure 1

13 pages, 8743 KiB  
Article
Genome-Wide Identification and Expression Analysis of Lipoxygenase Genes in Rose (Rosa chinensis)
by Wenqi Dong, Bo Jiao, Jiao Wang, Lei Sun, Songshuo Li, Zhiming Wu, Junping Gao and Shuo Zhou
Genes 2023, 14(10), 1957; https://doi.org/10.3390/genes14101957 - 18 Oct 2023
Viewed by 1033
Abstract
Lipoxygenases (LOX) play pivotal roles in plant resistance to stresses. However, no study has been conducted on LOX gene identification at the whole genome scale in rose (Rosa chinensis). In this study, a total of 17 RcLOX members were identified in [...] Read more.
Lipoxygenases (LOX) play pivotal roles in plant resistance to stresses. However, no study has been conducted on LOX gene identification at the whole genome scale in rose (Rosa chinensis). In this study, a total of 17 RcLOX members were identified in the rose genome. The members could be classified into three groups: 9-LOX, Type I 13-LOX, and Type II 13-LOX. Similar gene structures and protein domains can be found in RcLOX members. The RcLOX genes were spread among all seven chromosomes, with unbalanced distributions, and several tandem and proximal duplication events were found among RcLOX members. Expressions of the RcLOX genes were tissue-specific, while every RcLOX gene could be detected in at least one tissue. The expression levels of most RcLOX genes could be up-regulated by aphid infestation, suggesting potential roles in aphid resistance. Our study offers a systematic analysis of the RcLOX genes in rose, providing useful information not only for further gene cloning and functional exploration but also for the study of aphid resistance. Full article
(This article belongs to the Section Plant Genetics and Genomics)
Show Figures

Figure 1

14 pages, 1683 KiB  
Review
Hereditary Thrombotic Thrombocytopenic Purpura
by Sanober Nusrat, Kisha Beg, Osman Khan, Arpan Sinha and James George
Genes 2023, 14(10), 1956; https://doi.org/10.3390/genes14101956 - 18 Oct 2023
Cited by 1 | Viewed by 4321
Abstract
Hereditary thrombotic thrombocytopenic purpura (hTTP), also known as Upshaw–Schulman syndrome, is a rare genetic disorder caused by mutations in the ADAMTS13 gene that leads to decreased or absent production of the plasma von Willebrand factor (VWF)-cleaving metalloprotease ADAMTS13. The result is circulating ultra-large [...] Read more.
Hereditary thrombotic thrombocytopenic purpura (hTTP), also known as Upshaw–Schulman syndrome, is a rare genetic disorder caused by mutations in the ADAMTS13 gene that leads to decreased or absent production of the plasma von Willebrand factor (VWF)-cleaving metalloprotease ADAMTS13. The result is circulating ultra-large multimers of VWF that can cause microthrombi, intravascular occlusion and organ damage, especially at times of turbulent circulation. Patients with hTTP may have many overt or clinically silent manifestations, and a high index of suspicion is required for diagnosis. For the treatment of hTTP, the goal is simply replacement of ADAMTS13. The primary treatment is prophylaxis with plasma infusions or plasma-derived factor VIII products, providing sufficient ADAMTS13 to prevent acute episodes. When acute episodes occur, prophylaxis is intensified. Recombinant ADAMTS13, which is near to approval, will immediately be the most effective and also the most convenient treatment. In this review, we discuss the possible clinical manifestations of this rare disease and the relevant differential diagnoses in different age groups. An extensive discussion on prophylaxis and treatment strategies is also presented. Unique real patient cases have been added to highlight critical aspects of hTTP manifestations, diagnosis and treatment. Full article
(This article belongs to the Special Issue Diagnosis and Therapies for Genetic Diseases)
Show Figures

Figure 1

10 pages, 255 KiB  
Article
APOE Polymorphism Is Associated with Changes in the Kynurenine Pathway
by Per G. Farup, Helge Rootwelt and Knut Hestad
Genes 2023, 14(10), 1955; https://doi.org/10.3390/genes14101955 - 18 Oct 2023
Viewed by 989
Abstract
Background: APOE polymorphism and the Kynurenine pathway (KP) are associated with many disorders, but little is known about associations between APOE polymorphism and the KP. This study explored the associations between the KP and APOE polymorphism in disorders associated with APOE polymorphism and [...] Read more.
Background: APOE polymorphism and the Kynurenine pathway (KP) are associated with many disorders, but little is known about associations between APOE polymorphism and the KP. This study explored the associations between the KP and APOE polymorphism in disorders associated with APOE polymorphism and changes in the KP. Methods: Subjects with morbid obesity before and after bariatric surgery (numbers 139 and 95, respectively), depression (number 49), and unspecified neurological symptoms (number 39) were included. The following grouping of the APOE genotypes was used: E2 = ɛ2ɛ2 + ɛ2ɛ3, E3 = ɛ3ɛ3 + ɛ2ɛ4, and E4 = ɛ3ɛ4 + ɛ4ɛ4. The KP metabolites Tryptophan, Kynurenine, Kynurenic acid, Quinolinic acid, and Xanthurenic acid were quantified in serum. Results: The main findings were a significant positive association between E3 and Quinolinic acid (difference between E3 and E2E4: 12.0 (3.5; 18.6) ng/mL); p = 0.005), and a negative association between E4 and Kynurenine (difference between E4 and E2E3: −31.3 (−54.2; −3.2) ng/mL; p = 0.008). Quinolinic acid has been ascribed neurotoxic and inflammatory effects, and Kynurenine is a marker of inflammation. Conclusions: The findings indicate that APOE polymorphism might cause changes in the KP that contribute to the disease. Inflammation could be the link between APOE and the KP. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
12 pages, 275 KiB  
Review
The Role of miRNA Expression Profile in Sudden Cardiac Death Cases
by Alessia Bernini Di Michele, Valerio Onofri, Mauro Pesaresi and Chiara Turchi
Genes 2023, 14(10), 1954; https://doi.org/10.3390/genes14101954 - 17 Oct 2023
Viewed by 1261
Abstract
Sudden cardiac death (SCD) is one of the leading causes of death in the world and for this reason it has attracted the attention of numerous researchers in the field of legal medicine. It is not easy to determine the cause in a [...] Read more.
Sudden cardiac death (SCD) is one of the leading causes of death in the world and for this reason it has attracted the attention of numerous researchers in the field of legal medicine. It is not easy to determine the cause in a SCD case and the available methods used for diagnosis cannot always give an exhaustive answer. In addition, the molecular analysis of genes does not lead to a clear conclusion, but it could be interesting to focus attention on the expression level of miRNAs, a class of non-coding RNA of about 22 nucleotides. The role of miRNAs is to regulate the gene expression through complementary binding to 3′-untraslated regions of miRNAs, leading to the inhibition of translation or to mRNA degradation. In recent years, several studies were performed with the aim of exploring the use of these molecules as biomarkers for SCD cases, and to also distinguish the causes that lead to cardiac death. In this review, we summarize experiments, evidence, and results of different studies on the implication of miRNAs in SCD cases. We discuss the different biological starting materials with their respective advantages and disadvantages, studying miRNA expression on tissue (fresh-frozen tissue and FFPE tissue), circulating cell-free miRNAs in blood of patients affected by cardiac disease at high risk of SCD, and exosomal miRNAs analyzed from serum of people who died from SCD. Full article
(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)
29 pages, 5257 KiB  
Review
Molecular Mechanisms Underpinning Immunometabolic Reprogramming: How the Wind Changes during Cancer Progression
by Irene Flati, Mauro Di Vito Nolfi, Francesca Dall'Aglio, Davide Vecchiotti, Daniela Verzella, Edoardo Alesse, Daria Capece and Francesca Zazzeroni
Genes 2023, 14(10), 1953; https://doi.org/10.3390/genes14101953 - 17 Oct 2023
Viewed by 1589
Abstract
Metabolism and the immunological state are intimately intertwined, as defense responses are bioenergetically expensive. Metabolic homeostasis is a key requirement for the proper function of immune cell subsets, and the perturbation of the immune–metabolic balance is a recurrent event in many human diseases, [...] Read more.
Metabolism and the immunological state are intimately intertwined, as defense responses are bioenergetically expensive. Metabolic homeostasis is a key requirement for the proper function of immune cell subsets, and the perturbation of the immune–metabolic balance is a recurrent event in many human diseases, including cancer, due to nutrient fluctuation, hypoxia and additional metabolic changes occurring in the tumor microenvironment (TME). Although much remains to be understood in the field of immunometabolism, here, we report the current knowledge on both physiological and cancer-associated metabolic profiles of immune cells, and the main molecular circuits involved in their regulation, highlighting similarities and differences, and emphasizing immune metabolic liabilities that could be exploited in cancer therapy to overcome immune resistance. Full article
(This article belongs to the Special Issue Cell Signalling and Inflammation in Cancer)
Show Figures

Figure 1

8 pages, 4334 KiB  
Case Report
Clinical Case Report of Non-Diabetic Hypoglycemia Due to a Combination of Germline Mutations in the MEN1 and ABCC8 Genes
by Marina Yukina, Ekaterina Solodovnikova, Sergey Popov, Victorya Zakharova, Marina Utkina, Vasiliy Petrov, Ekaterina Troshina and Natalia Mokrysheva
Genes 2023, 14(10), 1952; https://doi.org/10.3390/genes14101952 - 17 Oct 2023
Viewed by 1048
Abstract
Introduction: Non-diabetic hypoglycemia (NDH) is a collective term including the multiple causes of hypoglycemic syndrome not due to diabetes mellitus. NDH may result from insulinoma, IGF-2-omas, hypocorticism, Hirata’s disease, genital disorders of glucose metabolism, etc. One of the most common causes of NDH [...] Read more.
Introduction: Non-diabetic hypoglycemia (NDH) is a collective term including the multiple causes of hypoglycemic syndrome not due to diabetes mellitus. NDH may result from insulinoma, IGF-2-omas, hypocorticism, Hirata’s disease, genital disorders of glucose metabolism, etc. One of the most common causes of NDH faced by an endocrinologist is insulinoma, which in turn can be part of the hereditary syndrome of multiple endocrine neoplasia type 1 (MEN1). Congenital disorders of glucose metabolism in adult patients, on the contrary, are diagnosed extremely rarely, since they usually manifest in childhood. This article presents a unique clinical case of a patient with NDH and genetically verified MEN1 in combination with congenital hyperinsulinism due to an ABCC8 gene mutation. Case Report: A 43-year-old patient with hypoglycemic symptoms from childhood is presented, in whom multiple pancreatic tumors and fluctuations in glycemia from 38.7 mg/dL to 329.7 mg/dL (2.15 to 18.3 mmol/L) were detected in adulthood, but a mild course of hypoglycemic syndrome was noted. Numerous examinations that were performed to establish an accurate diagnosis are described, signs that served as a reason for expanding the complex of studies are indicated, possible pathogenetic mechanisms of the mild course of hypoglycemic syndrome and hyperglycemic conditions are discussed. Conclusion: This case report is original and highlights that we must always remain intolerant of the inexplicable. Conducting an extended gene study can help perform a correct diagnosis in complex cases. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
Show Figures

Figure 1

13 pages, 2000 KiB  
Article
Genome-Wide Analysis on Driver and Passenger RNA Editing Sites Suggests an Underestimation of Adaptive Signals in Insects
by Yuchen Zhang and Yuange Duan
Genes 2023, 14(10), 1951; https://doi.org/10.3390/genes14101951 - 17 Oct 2023
Cited by 4 | Viewed by 823
Abstract
Adenosine-to-inosine (A-to-I) RNA editing leads to a similar effect to A-to-G mutations. RNA editing provides a temporo-spatial flexibility for organisms. Nonsynonymous (Nonsyn) RNA editing in insects is over-represented compared with synonymous (Syn) editing, suggesting adaptive signals of positive selection on Nonsyn editing during [...] Read more.
Adenosine-to-inosine (A-to-I) RNA editing leads to a similar effect to A-to-G mutations. RNA editing provides a temporo-spatial flexibility for organisms. Nonsynonymous (Nonsyn) RNA editing in insects is over-represented compared with synonymous (Syn) editing, suggesting adaptive signals of positive selection on Nonsyn editing during evolution. We utilized the brain RNA editome of Drosophila melanogaster to systematically study the LD (r2) between editing sites and infer its impact on the adaptive signals of RNA editing. Pairs of editing sites (PESs) were identified from the transcriptome. For CDS PESs of two consecutive editing sites, their occurrence was significantly biased to type-3 PES (Syn-Nonsyn). The haplotype frequency of type-3 PES exhibited a significantly higher abundance of AG than GA, indicating that the rear Nonsyn site is the driver that promotes the editing of the front Syn site (passenger). The exclusion of passenger Syn sites dramatically amplifies the adaptive signal of Nonsyn RNA editing. Our study for the first time quantitatively demonstrates that the linkage between RNA editing events comes from hitchhiking effects and leads to the underestimation of adaptive signals for Nonsyn editing. Our work provides novel insights for studying the evolutionary significance of RNA editing events. Full article
(This article belongs to the Special Issue RNAs in Biology)
Show Figures

Figure 1

15 pages, 6887 KiB  
Article
Identification of the RPGR Gene Pathogenic Variants in a Cohort of Polish Male Patients with Retinitis Pigmentosa Phenotype
by Katarzyna Nowomiejska, Katarzyna Baltaziak, Paulina Całka, Marzanna Ciesielka, Grzegorz Teresiński and Robert Rejdak
Genes 2023, 14(10), 1950; https://doi.org/10.3390/genes14101950 - 17 Oct 2023
Viewed by 891
Abstract
The goal of the study was to explore the spectrum of pathogenic variants in the RPGR gene in a group of male Polish patients with a retinitis pigmentosa (RP) phenotype. A total of 45 male index patients, including twins, being members of 44 [...] Read more.
The goal of the study was to explore the spectrum of pathogenic variants in the RPGR gene in a group of male Polish patients with a retinitis pigmentosa (RP) phenotype. A total of 45 male index patients, including twins, being members of 44 families, were screened for pathogenic variants in the RPGR gene via the direct sequencing of PCR-amplified genomic DNA and underwent a comprehensive ophthalmological examination in one center located in Poland. A total of two pathogenic and five likely pathogenic variants in eight patients (18%) were detected in the studied cohort. Of these, five variants were novel, and five disease-causing variants (71%) were identified within the ORF15 mutational hotspot of the RPGR gene. The median age of onset of the disease was 10 years (range 6–14 years), the median age during the examination was 30 years (range 20–47 years), and the median visual acuity was 0.4 (range 0.01–0.7). The majority of patients had middle constriction of the visual field and thinning of the central foveal thickness. Dizygotic twins bearing the same hemizygous mutation showed a different retinal phenotype in regard to the severity of the symptoms. This is the first RPGR mutation screening in Poland showing a prevalence of 18% of RPGR pathogenic mutations and likely pathogenic variants in the studied cohort of male patients with an RP phenotype. Full article
(This article belongs to the Special Issue Genetics in Inherited Retinal Diseases)
Show Figures

Figure 1

13 pages, 3053 KiB  
Article
Identification of Intron Retention in the Slc16a3 Gene Transcript Encoding the Transporter MCT4 in the Brain of Aged and Alzheimer-Disease Model (APPswePS1dE9) Mice
by Ayman EL-Seedy, Luc Pellerin, Guylène Page and Veronique Ladeveze
Genes 2023, 14(10), 1949; https://doi.org/10.3390/genes14101949 - 17 Oct 2023
Viewed by 1259
Abstract
The monocarboxylate transporter 4 (MCT4; Slc16a3) is expressed in the central nervous system, notably by astrocytes. It is implicated in lactate release and the regulation of glycolytic flux. Whether its expression varies during normal and/or pathological aging is unclear. As the presence of [...] Read more.
The monocarboxylate transporter 4 (MCT4; Slc16a3) is expressed in the central nervous system, notably by astrocytes. It is implicated in lactate release and the regulation of glycolytic flux. Whether its expression varies during normal and/or pathological aging is unclear. As the presence of its mature transcript in the brain of young and old mice was determined, an unexpectedly longer RT-PCR fragment was detected in the mouse frontal cortex and hippocampus at 12 vs. 3 months of age. Cultured astrocytes expressed the expected 516 base pair (bp) fragment but treatment with IL-1β to mimic inflammation as can occur during aging led to the additional expression of a 928 bp fragment like that seen in aged mice. In contrast, cultured pericytes (a component of the blood–brain barrier) only exhibited the 516 bp fragment. Intriguingly, cultured endothelial cells constitutively expressed both fragments. When RT-PCR was performed on brain subregions of an Alzheimer mouse model (APPswePS1dE9), no fragment was detected at 3 months, while only the 928 bp fragment was present at 12 months. Sequencing of MCT4 RT-PCR products revealed the presence of a remaining intron between exon 2 and 3, giving rise to the longer fragment detected by RT-PCR. These results unravel the existence of intron retention for the MCT4 gene in the central nervous system. Such alternative splicing appears to increase with age in the brain and might be prominent in neurodegenerative diseases such as Alzheimer’s disease. Hence, further studies in vitro and in vivo of intron 2 retention in the Slc16a3 gene transcript are required for adequate characterization concerning the biological roles of Slc16a3 isoforms in the context of aging and Alzheimer’s disease pathology. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
Show Figures

Graphical abstract

Previous Issue
Next Issue
Back to TopTop