Genes, Volume 13, Issue 11 (November 2022) – 257 articles

Lynch syndrome (LS) is the most common cause of hereditary colorectal cancers (CRC) and is associated with an increased risk for ovarian and endometrial cancers. There is lack of knowledge on the epidemiology of LS in the non-Caucasian populations especially in Qatar. The aim of this retrospective study is to explore the prevalence of LS in a selected high-risk cohort in the State of Qatar in addition to investigating the frequency and genotype-phenotype correlation associated with mismatch repair genes pathogenic variants. Retrospective review of medical records of 31 individuals with LS, 20 affected with colorectal cancer and 11 unaffected with family history of cancers, referred from January 2017 until August 2020. The prevalence of LS among affected and unaffected patients is 22% (20/92) and 2.2% respectively. Among affected individuals, MLH1 and MSH2 genes were highly frequent while for unaffected individuals, a recurrent PMS2 pathogenic variant was reported in several related individuals suggesting a tribal effect. This study highlights the epidemiology of LS in high-risk cohort in Qatar which helps to provide recommendations on genetic testing, and personalize surveillance and management programs Full article

An increase in the number of vertebrae can significantly affect the meat production performance of livestock, thus increasing carcass weight, which is of great importance for livestock production. The homeobox gene C8 (HOXC8) has been identified as an essential candidate gene for regulating vertebral development. However, it has not been researched on the Dezhou donkey. This study aimed to verify the Dezhou donkey HOXC8 gene’s polymorphisms and assess their effects on multiple vertebral numbers and carcass weight. In this study, the entire HOXC8 gene of the Dezhou donkey was sequenced, SNPs at the whole gene level were identified, and typing was accomplished utilizing a targeted sequencing genotype detection technique (GBTS). Then, a general linear model was used to perform an association study of HOXC8 gene polymorphism loci, multiple vertebral numbers, and carcass weight for screening candidate markers that can be used for molecular breeding of Dezhou donkeys. These findings revealed that HOXC8 included 12 SNPs, all unique mutant loci. The HOXC8 g.15179224C>T was significantly negatively associated with carcass weight (CW) and lumbar vertebrae length (LL) (p < 0.05). The g.15179674G>A locus was shown to be significantly positively associated with the number of lumbar vertebrae (LN) (p < 0.05). The phylogenetic tree constructed for the Dezhou donkey HOXC8 gene and seven other species revealed that the HOXC8 gene was highly conserved during animal evolution but differed markedly among distantly related animals. The results suggest that HOXC8 is a vital gene affecting multiple vertebral numbers and carcass weight in Dezhou donkeys, and the two loci g.15179224C>T and g.15179674G>A may be potential genetic markers for screening and breeding of new strains of high-quality and high-yielding Dezhou donkeys. Full article

Dementia has enormous implications for patients and the health care system. Genetic markers are promising for detecting the risk of cognitive impairment. We hypothesized that genetic variants associated with suicide risk might significantly increase the risk of cognitive decline because suicide in older adults is often a consequence of cognitive impairment. We investigated several single-nucleotide polymorphisms that were initially associated with suicide risk in dementia older adults and identified the APOE gene alleles. The study was performed with subjects over the age of 65: 112 patients with dementia and 146 healthy volunteers. The MMSE score was used to assess cognitive functions. Study participants were genotyped using real-time PCR (APOE: rs429358, rs7412; genes associated with suicide: rs9475195, rs7982251, rs2834789, rs358592, rs4918918, rs3781878, rs10903034, rs165774, rs16841143, rs11833579 rs10898553, rs7296262, rs3806263, and rs2462021). Genotype analysis revealed the significance of APOEε4, APOEε2, and rs4918918 (SORBS1) when comparing dementia and healthy control groups. The association of APOEε4, APOEε2, and rs10903034 (IFNLR1) with the overall MMSE score was indicated. The study found an association with dementia of rs4918918 (SORBS1) and rs10903034 (IFNLR1) previously associated with suicide and confirmed the association of APOEε4 and APOEε2 with dementia. Full article

Cystinuria is a genetically inherited disorder of renal and intestinal transport, featured as a high concentration of cystine in the urine. Cumulative cystine in urine would cause the formation of kidney stones, which further leads to renal colic and dysfunction. Gene screens have found that mutations in SLC3A1 or SLC7A9 gene are responsible for most cases of cystinuria, for encoding defective cystine transporters. Here, we presented the genotypic and phenotypic characteristics of one unique case of a three-generation Chinese family. The proband developed severe urolithiasis combined with renal damage. The radiography and computed tomography (CT) scan showed calculus in the left pelvic kidney. Postoperative stone analysis revealed that the stones were mainly composed of cystine. Therefore, to explore its pathogenesis, next-generation Whole Exome Sequencing (WES) and Sanger sequencing identify the proband mutated gene of the proband’s family. In this article, we reported novel compound heterozygous mutations (c.818G>A and c.1011G>A) of the SLC3A1 gene in a 5-year-old child suffering from a cystine stone from a three-generation family. Bioinformatic analysis was used to predict the pathogenicity and conservation of the target mutation. Conservative sequence and evolutionary conservation analysis indicated that cystine²⁷³ and proline³³⁷ were highly conserved among species, and both mutations listed here (Cys273Tyr and Pro337Pro) were pathogenic. To conclude, our study expands the phenotypic and genotypic spectrum of SLC3A1 and indicates that genetic screening should be considered in the clinic to provide more effective and precise treatment for cystinuria. Full article

Apelin, a peptide initially isolated from bovine stomach extract, is an endogenous ligand for the Apelin Receptor (APLNR). Subsequently, a second peptide, ELABELA, that can bind to the receptor has been identified. The Apelin receptor and its endogenous ligands are widely distributed in mammalian organs. A growing body of evidence suggests that this system participates in various signaling cascades that can regulate cell proliferation, blood pressure, fluid homeostasis, feeding behavior, and pituitary hormone release. Additional research has been done to elucidate the system’s potential role in neurogenesis, the pathophysiology of Glioblastoma multiforme, and the protective effects of apelin peptides on some neurological and psychiatric disorders-ischemic stroke, epilepsy, Parkinson’s, and Alzheimer’s disease. This review discusses the current knowledge on the apelinergic system’s involvement in brain physiology in health and disease. Full article

The National Institute of Standards and Technology has released a document entitled DNA Mixture Interpretation: A NIST Scientific Foundation Review for public comment. This has become known as the Draft NIST Foundation Review. It contains the statement: “Across these 69 data sets, there were 80 false negatives and 18 false positives reported from 110,408 possible responses (27,602 participants × two evidence items × two reference items). In the past five years, the number of participants using PGS has grown.” We examine a set of proficiency test results to determine if these NIST statements could be justified. The summary reports for each relevant forensic biology test (Forensic Biology, Semen, and Mixture) in the years 2018–2021 were reviewed. Data were also provided to us by CTS upon our request. None of the false positives or negatives could be attributed to the mixture interpretation strategy and certainly not to the use of PGS. Full article

As global climate change worsens, trees will have difficulties adapting to abiotic pressures, particularly in the field, where environmental characteristics are difficult to control. A prospective commercial and ornamental tree species, Styrax tonkinensis, has its seed oil output and quality reduced as a result, which lowers the economic benefits. This necessitates growers to implement efficient strategies to increase the seeds of woody biofuel species’ tolerance to abiotic stress. Numerous studies have shown that ZnO nanoparticles (NPs), a new material, and BRs assist plants to increase their resilience to abiotic stress and subsequently adapt to it. However, there have not been many investigations into S. tonkinensis seed resistance. In this study, we examined the changes in antioxidant enzyme activities and transcriptomic results of S. tonkinensis seeds throughout the seed development period to investigate the effects of 24-epibrassinolide (EBL), one of the BRs, and ZnO NPs treatments alone or together on the stress resistance of S. tonkinensis seeds. On 70, 100, and 130 days after flowering (DAF), spraying EBL or ZnO NPs increased the activity of antioxidant enzymes (POD, SOD, and CAT) in S. tonkinensis seeds. Moreover, when the EBL and ZnO NPs were sprayed together, the activities of antioxidant enzymes were the strongest, which suggests that the positive effects of the two can be superimposed. On 70 and 100 DAF, the EBL and ZnO NPs treatments improved seed stress resistance, mostly through complex plant hormone crosstalk signaling, which includes IAA, JA, BR, and ABA signaling. Additionally, ABA played an essential role in hormone crosstalk, while, on 130 DAF, due to the physiological characteristics of seeds themselves in the late stage of maturity, the improvement in seed stress resistance by EBL and ZnO NPs was related to protein synthesis, especially late embryogenesis-abundant protein (LEA), and other nutrient storage in seeds. Spraying EBL and ZnO NPs during the seed growth of S. tonkinensis could significantly increase seed stress resistance. Our findings provide fresh perspectives on how cultural practices can increase abiotic stress tolerance in woody seedlings. Full article

Ageing is defined by the decline in the biological and physiological functions over time, which leads to health problems and increases risks of diseases. The modern societies are characterised by an ageing population, which represents challenges for the healthcare system. Within this context, there is a need to better understand the biological mechanisms beyond ageing in order to optimise geriatric therapies and medical approaches. Herein, we suggest exploring the genetic and epigenetic patterns related to ageing and correlate them with the ageing-related phenotype of the biological entities in order to establish mechanistic links and map the molecular pathways. Such links would have diverse implications in basic research, in clinics, as well as for therapeutic studies. Full article

The purpose of this study is to explore the correlation between ferroptosis-related genes and schizophrenia in order to explore the new direction of diagnosis and treatment of schizophrenia. We screened the datasets related to schizophrenia from the Gene Expression Comprehensive Database (GEO) and obtained ferroptosis-related genes from the FerrDB database. Bioinformatics methods were used to analyze differentially expressed genes (DEGs) and genes associated with ferroptosis-related between schizophrenia patients and healthy controls. On this basis, the hub genes were finally screened by enrichment analysis and PPI interaction analysis. Hub genes associated with ferroptosis were validated using other schizophrenia datasets in the GEO database. Finally, the hub gene-microRNA (miRNA), gene-transcription factor interaction network was constructed, and three ferroptosis-related hub genes (TP53, VEGFA and PTGS2) were screened. The validation results of these three genes in other datasets also support this conclusion. A miRNA: hsa-mir-16-5p was found to be related to the three hub genes, and pPHF8, SAP30 and lKDM5B were identified as common regulators of the three hub genes. Our results indicate that TP53, VEGFA and PTGS2 are significantly associated with schizophrenia, and may be ferroptosis-related markers of the disease. Full article

Disease-associated pathogenic variants in the A-Kinase Anchor Protein 9 (AKAP9) (MIM *604001) have been recently identified in patients with autosomal dominant long QT syndrome 11 (MIM #611820), lethal arrhythmia (ventricular fibrillation, polymorphic ventricular tachycardia), Brugada syndrome, and sudden unexpected death. However, AKAP9 sequence variations were rarely reported and AKAP9 was classified as a “disputed evidence” gene to support disease causation due to the insufficient genetic evidence and a limited number of reported AKAP9-mutated patients. Here, we describe a 47-year-old male carrying a novel frameshift AKAP9 pathogenic variant who presented recurrent syncopal attacks and sudden cardiac arrest that required a semi-automatic external defibrillator implant and an electric shock treatment of ventricular arrhythmia. This study provides insight into the mechanism underlying cardiac arrest and confirms that AKAP9 loss-of-function variants predispose to serious, life-threatening ventricular arrhythmias. Full article

Background: Up frameshift protein 1 (UPF1) is a key component of nonsense-mediated mRNA decay (NMD) of mRNA containing premature termination codons (PTCs). The dysregulation of UPF1 has been reported in various cancers. However, the expression profile of UPF1 and its clinical significance in clear cell renal cell carcinoma (ccRCC) remains unclear. Methods: In order to detect UPF1 expression in ccRCC and its relationship with the clinical features of ccRCC, bulk RNA sequencing data were analyzed from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and ArrayExpress databases. The impact of UPF1 on the immune microenvironment of ccRCC was evaluated by multiple immune scoring algorithms to identify the cell groups that typically express UPF1 using ccRCC single cell sequencing (scRNA) data. In addition, genes co-expressed with UPF1 were identified by the weighted gene correlation network analysis (WGCNA), followed by KEGG and Reactome enrichment analysis. A series of functional experiments were performed to assess the roles of UPF1 in renal cancer cells. Finally, pan-cancer analysis of UPF1 was also performed. Results: Compared with normal tissues, the expression levels of UPF1 mRNA and protein in tumor tissues of ccRCC patients decreased significantly. In addition, patients with low expression of UPF1 had a worse prognosis. Analysis of the immune microenvironment indicated that UPF1 immune cell infiltration was closely related and the ccRCC scRNA-seq data identified that UPF1 was mainly expressed in macrophages. WGCNA analysis suggested that the functions of co-expressed genes are mainly enriched in cell proliferation and cellular processes. Experimental tests showed that knockdown of UPF1 can promote the invasion, migration and proliferation of ccRCC cells. Lastly, pan-cancer analysis revealed that UPF1 disorders were closely associated with various cancer outcomes. Conclusions: UPF1 may play a tumor suppressive role in ccRCC and modulate the immune microenvironment. The loss of UPF1 can predict the prognosis of ccRCC, making it a promising biomarker and providing a new reference for prevention and treatment. Full article

Cannabidiol (CBD) is a non-psychotomimetic compound present in cannabis sativa. Many recent studies have indicated that CBD has a promising therapeutic profile for stress-related psychiatric disorders, such as anxiety, schizophrenia and depression. Such a diverse profile has been associated with its complex pharmacology, since CBD can target different neurotransmitter receptors, enzymes, transporters and ion channels. However, the precise contribution of each of those mechanisms for CBD effects is still not yet completely understood. Considering that epigenetic changes make the bridge between gene expression and environment interactions, we review and discuss herein how CBD affects one of the main epigenetic mechanisms associated with the development of stress-related psychiatric disorders: DNA methylation (DNAm). Evidence from in vivo and in silico studies indicate that CBD can regulate the activity of the enzymes responsible for DNAm, due to directly binding to the enzymes and/or by indirectly regulating their activities as a consequence of neurotransmitter-mediated signaling. The implications of this new potential pharmacological target for CBD are discussed in light of its therapeutic and neurodevelopmental effects. Full article

An assessment of the genetic diversity and structure of a population is essential for designing recovery plans for threatened species. Italy hosts two brown bear populations, Ursus arctos marsicanus (Uam), endemic to the Apennines of central Italy, and Ursus arctos arctos (Uaa), in the Italian Alps. Both populations are endangered and occasionally involved in human–wildlife conflict; thus, detailed management plans have been in place for several decades, including genetic monitoring. Here, we propose a simple cost-effective microsatellite-based protocol for the management of populations with low genetic variation. We sampled 22 Uam and 22 Uaa individuals and analyzed a total of 32 microsatellite loci in order to evaluate their applicability in individual identification. Based on genetic variability estimates, we compared data from four different STR marker sets, to evaluate the optimal settings in long-term monitoring projects. Allelic richness and gene diversity were the highest for the Uaa population, whereas depleted genetic variability was noted for the Uam population, which should be regarded as a conservation priority. Our results identified the most effective STR sets for the estimation of genetic diversity and individual discrimination in Uam (9 loci, PIC 0.45; PID 2.0 × 10⁻⁵), and Uaa (12 loci, PIC 0.64; PID 6.9 × 10⁻¹¹) populations, which can easily be utilized by smaller laboratories to support local governments in regular population monitoring. The method we proposed to select the most variable markers could be adopted for the genetic characterization of other small and isolated populations. Full article

Background: Inactivating NSD1 mutations causing Sotos syndrome have been previously associated with a specific genome-wide DNA methylation (DNAm) pattern. Sotos syndrome is characterized by phenotypic overlap with other overgrowth syndromes, and a definite diagnosis might not be easily reached due to the high prevalence of variants of unknown significance (VoUS) that are identified in patients with a suggestive phenotype. Objective: we performed microarray DNAm profiling in a set of 11 individuals with a clinical suspicion of Sotos syndrome and carrying an NSD1 VoUS or previously unreported variants to solve uncertainty in defining pathogenicity of the observed variants. The impact of the training cohort size on sensitivity and prediction confidence of the classifier was assessed. Results: The Sotos syndrome-specific DNAm signature was validated in six individuals with a clinical diagnosis of Sotos syndrome and carrying bona fide pathogenic NSD1 variants. Applying this approach to the remaining 11 individuals with NSD1 variants, we succeeded in confirming pathogenicity in eight subjects and excluding the diagnosis of Sotos syndrome in three. The sensitivity and prediction confidence of the classifier based on the different sizes of the training sets did not show substantial differences, though the overall performance was improved by using a data balancing strategy. Conclusions: The present approach solved uncertainty in cases with NDS1 VoUS, further demonstrating the clinical utility of DNAm profiling. Full article

Oil-tea camellia trees, the collective term for a class of economically valuable woody oil crops in China, have attracted extensive attention because of their rich nutritional and pharmaceutical value. This study aimed to analyze the genetic relationship and genetic diversity of oil-tea camellia species using polymorphic SSR markers. One-hundred and forty samples of five species were tested for genetic diversity using twenty-four SSR markers. In this study, a total of 385 alleles were identified using 24 SSR markers, and the average number of alleles per locus was 16.0417. The average Shannon’s information index (I) was 0.1890, and the percentages of polymorphic loci (P) of oil-tea camellia trees were 7.79−79.48%, indicating that oil-tea camellia trees have low diversity. Analysis of molecular variance (AMOVA) showed that the majority of genetic variation (77%) was within populations, and a small fraction (23%) occurred among populations. Principal coordinate analysis (PCoA) results indicated that the first two principal axes explained 7.30% (PC1) and 6.68% (PC2) of the total variance, respectively. Both UPGMA and PCoA divided the 140 accessions into three groups. Camellia oleifera clustered into one class, Camellia vietnamensis and Camellia gauchowensis clustered into one class, and Camellia crapnelliana and Camellia chekiangoleosa clustered into another class. It could be speculated that the genetic relationship of C. vietnamensis and C. gauchowensis is quite close. SSR markers could reflect the genetic relationship among oil-tea camellia germplasm resources, and the results of this study could provide comprehensive information on the conservation, collection, and breeding of oil-tea camellia germplasms. Full article

To evaluate differences among 19 different ploidy hybrid poplar clones grown in northeast China, 21 traits related to growth traits and photosynthetic characteristics were detected and analyzed. Abundant phenotypic variations exist among and within populations, and these variations are the basis of forest tree genetic improvements. In this research, variance analysis showed that the traits except the net photosynthesis rate among the different ploidies and all the other traits exhibited significant differences among the ploidies or clones (p < 0.01). Estimation of phenotypic coefficients of variation, genotypic coefficients of variation, and repeatability is important for selecting superior materials. The larger the value, the greater the potential for material selection improvement. The repeatability of the different traits ranged from 0.88 to 0.99. The phenotypic and genotypic coefficients of variation of all the investigated traits ranged from 6.88% to 57.40% and from 4.85% to 42.89%, respectively. Correlation analysis showed that there were significant positive correlations between tree height, diameter, and volume. Transpiration rate, intercellular carbon dioxide concentration, and stomatal conductance were significantly positively correlated with each other but negatively correlated with instantaneous water use efficiency. Growth traits were weakly correlated with photosynthetic indexes. The rank correlation coefficient showed that most of the growth indicators reached a significant correlation level among different years (0.40–0.98), except 1-year-old tree height with 4-year-old tree height and 1-year-old ground diameter with 3-year-old tree height, which indicated the potential possibility for early selection of elite clones. Principal analysis results showed that the contribution rate of the first principal component was 46.606%, and 2-year-old tree height, 2-year-old ground diameter, 3-year-old tree height, 3-year-old ground diameter, 3-year-old diameter at breast height, 3-year-old volume, 4-year-old tree height, 4-year-old ground diameter, 4-year-old diameter at breast height, and 4-year-old volume showed higher vector values than other traits. With the method of multiple-trait comprehensive evaluation to evaluate clones, SX3.1, SY3.1, and XY4.2 were selected as elite clones, and the genetic gains of height, basal diameter, diameter at breast height, and volume of selected clones ranged from 12.85% to 64.87% in the fourth growth year. The results showed fundamental information for selecting superior poplar clones, which might provide new materials for the regeneration and improvement of forests in Northeast China. Full article

The growing prevalence of antibiotic-resistant Staphylococcus aureus strains mandates selective susceptibility testing and epidemiological investigations. It also draws attention to an efficient typing strategy. Whole genome sequencing helps in genetic comparison, strain differentiation, and typing; however, it is not that cost-effective. In comparison, Multi-Locus Sequence Typing (MLST) is an efficient typing method employed for bacterial strain typing and characterizations. In this paper, a comprehensive pangenome and phylogenetic analysis of 502/1279 S. aureus genomes is carried out to understand the species divergence. Additionally, the current Multi-Locus Sequence Typing (MLST) scheme was evaluated, and genes were excluded or substituted by alternative genes based on reported shortcomings, genomic data, and statistical scores calculated. The data generated were helpful in devising a new Multi-Locus Sequence Typing (MLST) scheme for the efficient typing of S. aureus strains. The revised scheme is now a blend of previously used genes and new candidate genes. The genes yQil, aroE, and gmk are replaced with better gene candidates, opuCC, aspS, and rpiB, based on their genome localization, representation, and statistical scores. Therefore, the proposed Multi-Locus Sequence Typing (MLST) method offers a greater resolution with 58 sequence types (STs) in comparison to the prior scheme’s 42 STs. Full article

Lung and breast cancer are the two most common causes of malignant pleural effusion (MPE). MPE diagnosis plays a crucial role in determining staging and therapeutic interventions in these cancers. However, our understanding of the pathogenesis and progression of MPE at the molecular level is limited. Extracellular Vesicles (EVs) and their contents, including microRNAs (miRNAs), can be isolated from all bodily fluids, including pleural fluid. This study aims to compare EV-miRNA patterns of expression in MPE caused by breast (BA-MPE) and lung (LA-MPE) adenocarcinomas compared to the control group of heart-failure-induced effusions (HF-PE). We conducted an analysis of 24 pleural fluid samples (8 LA-MPE, 8 BA-MPE, and 8 HF-PE). Using NanoString technology, we profiled miRNAs within EVs isolated from 12 cases. Bioinformatic analysis demonstrated differential expression of miR-1246 in the MPE group vs. HF-PE group and miR-150-5p and miR-1246 in the BA-MPE vs. LA-MPE group, respectively. This difference was demonstrated and validated in an independent cohort using real-time PCR (RT-PCR). miRNA-1246 demonstrated 4-fold increased expression (OR: 3.87, 95% CI: 0.43, 35) in the MPE vs. HF-PE group, resulting in an area under the curve of 0.80 (95% CI: 0.60, 0.99). The highest accuracy for differentiating MPE vs. HF-PE was seen with a combination of miRNAs compared to each miRNA alone. Consistent with prior studies, this study demonstrates dysregulation of specific EV-based miRNAs in breast and lung cancer; pleural fluid provides direct access for the analysis of these EV-miRNAs as biomarkers and potential targets and may provide insight into the underlying pathogenesis of tumor progression. These findings should be explored in large prospective studies. Full article

Tissue fragility, skin hyperextensibility and joint hypermobility are defining characteristics of Ehlers–Danlos syndrome (EDS). Human EDS is subclassified into fourteen types including dermatosparactic EDS, characterized by extreme skin fragility and caused by biallelic ADAMTS2 mutations. We report two novel, ADAMTS2 variants in DNA from EDS-affected dogs. Separate whole-genome sequences from a Pit Bull Terrier and an Alapaha Blue Blood Bulldog each contained a rare, homozygous variant (11:2280117delC, CanFam3.1), predicted to produce a frameshift in the transcript from the first coding ADAMTS2 exon (c.10delC) and a severely truncated protein product, p.(Pro4ArgfsTer175). The clinical features of these dogs and 4 others with the same homozygous deletion included multifocal wounds, atrophic scars, joint hypermobility, narrowed palpebral fissures, skin hyperextensibility, and joint-associated swellings. Due to severe skin fragility, the owners of all 6 dogs elected euthanasia before the dogs reached 13 weeks of age. Cross sections of collagen fibrils in post-mortem dermal tissues from 2 of these dogs showed hieroglyphic-like figures similar to those from cases of severe dermatosparaxis in other species. The whole-genome sequence from an adult Catahoula Leopard Dog contained a homozygous ADAMTS2 missense mutation, [11:2491238G>A; p.(Arg966His)]. This dog exhibited multifocal wounds, atrophic scars, and joint hypermobility, but has survived for at least 9 years. This report expands the spectrum of clinical features of the canine dermatosparactic subtype of EDS and illustrates the potential utility of subclassifying canine EDS by the identity of gene harboring the causal variant. Full article

In natural sea areas along the coast of China, venerid clams Ruditapes philippinarum and R. variegatus exhibit similar adult shell forms and are especially difficult to distinguish as spat and juveniles. This study used comparative mitochondrial genome analysis to reveal differences between these species. The results showed that: (1) the mitochondrial genomes of R. philippinarum and R. variegatus share a large number of similar gene clusters arranged in consistent order, yet they also display noncommon genes, with both gene rearrangements and random losses found; (2) the 13 protein-coding genes in R. philippinarum as well as two-fold and four-fold degenerate sites in R. variegatus have an evident AT bias; (3) the Ka/Ks ratio of the mitochondrial ATP8 gene was significantly higher in R. philippinarum than in R. variegatus, and an analysis of selection pressure revealed that the mitochondrial NADH dehydrogenase subunit 2 gene and NADH dehydrogenase subunit 6 gene of R. variegatus were under great selective pressure during its evolution; and finally, (4) the two species clustered into one branch on a phylogenetic tree, further affirming their phylogenetic closeness. Based on these results, we speculate that the species differences between R. variegatus and R. philippinarum are largely attributable to adaptive evolution to the environment. The present findings provide a reference for the development of germplasm identification. Full article

Quercus (oak) is an important economic and ecological tree species in the world, and it is the necessary feed for oak silkworm feeding. Chloroplasts play an important role in green plants but the codon usage of oak chloroplast genomes is not fully studied. We examined the codon usage of the oak chloroplast genomes in detail to facilitate the understanding of their biology and evolution. We downloaded all the protein coding genes of 26 non-redundant chloroplast reference genomes, removed short ones and those containing internal stop codons, and finally retained 50 genes shared by all genomes for comparative analyses. The base composition, codon bias, and codon preference are not significantly different between genomes but are significantly different among genes within these genomes. Oak chloroplast genomes prefer T/A-ending codons and avoid C/G-ending codons, and the psbA gene has the same preference except for the codons encoding amino acid Phe. Complex factors such as context-dependent mutations are the major factors affecting codon usage in these genomes, while selection plays an important role on the psbA gene. Our study provided an important understanding of codon usage in the oak chloroplast genomes and found that the psbA gene has nearly the same codon usage preference as other genes in the oak chloroplasts. Full article

Existing approaches to predicting RNA secondary structures depend on how the secondary structure is decomposed into substructures, that is, the architecture, to define their parameter space. However, architecture dependency has not been sufficiently investigated, especially for pseudoknotted secondary structures. In this study, we propose a novel algorithm for directly inferring base-pairing probabilities with neural networks that do not depend on the architecture of RNA secondary structures, and then implement this approach using two maximum expected accuracy (MEA)-based decoding algorithms: Nussinov-style decoding for pseudoknot-free structures and IPknot-style decoding for pseudoknotted structures. To train the neural networks connected to each base pair, we adopt a max-margin framework, called structured support vector machines (SSVM), as the output layer. Our benchmarks for predicting RNA secondary structures with and without pseudoknots show that our algorithm outperforms existing methods in prediction accuracy. Full article

TARP syndrome (Talipes equinovarus, Atrial septal defect, Robin sequence, and Persistence of the left superior vena cava) is a rare genetic condition, caused by developmental defects during embryogenesis. The phenotypic spectrum of TARP shows high clinical variability with patients either missing cardinal features or having additional clinical traits. Initially, TARP was considered a lethal syndrome, but patients with milder symptoms were recently described. The TARP-locus was mapped to the gene RNA-binding motif protein 10 (RBM10) on the human X-chromosome. We clinically and genetically described a six-year-old boy with a TARP-phenotype. Clinical heterogeneity of symptoms prompted us to sequence the entire exome of this patient. We identified a novel splice variant (NM_005676: c.17+1G>C, p.?) in RBM10. A patient-derived cell line was used to verify the pathogenicity of the RBM10 splice variant by RNA analyses, Western blotting, and immunofluorescence staining. Our molecular genetic findings together with the analyses of progressing clinical symptoms confirmed the diagnosis of TARP. It seems essential to analyze correlations between genotype, phenotype, and molecular/cellular data to better understand RBM10-associated pathomechanisms, assist genetic counseling, and support development of therapeutic approaches. Full article

Native chicken has become a favorite choice for consumers in many Asian countries recently, not only for its potential nutritional value but also for its deep ties to local food culture. However, low growth performance and limited meat production restrict their economic potential. Conducting a genome-wide association study (GWAS) for chicken-breast muscle development will help identify loci or candidate genes for different traits and potentially provide new insight into this phenotype in chickens and other species. To improve native chicken growth performance, especially breast muscle development, we performed a GWAS to explore the potential genetic mechanisms of breast muscle development in an F2 population constructed by reciprocal crosses between a fast-growing broiler chicken (Cobb500) and a slow-growing native chicken (Daweishan mini chicken). The results showed that 11 SNPs, which exceeded the 10% genome significance level (p = 1.79 × 10⁻⁸) were considered associated with breast muscle development traits, where six SNPS, NC_006126.5: g.3138376T>G, NC_006126.5: g.3138452A>G, NC_006088.5: g.73837197A>G, NC_006088.5: g.159574275A>G, NC_006089.5: g.80832197A>G, and NC_006127.5: g.48759869G>T was first identified in this study. In total, 13 genes near the SNPs were chosen as candidate genes, and none of them had previously been studied for their role in breast muscle development. After grouping the F2 population according to partial SNPs, significant differences in breast muscle weight were found among different genotypes (p < 0.05), and the expression levels of ALOX5AP, USPL1, CHRNA9, and EFNA5 among candidate genes were also significantly different (p < 0.05). The results of this study will contribute to the future exploration of the potential genetic mechanisms of breast muscle development in domestic chickens and also support the expansion of the market for native chicken in the world. Full article

The incidence of liver cancer ranks seventh globally, with nearly half of all cases occurring in East Asia, but currently, there are very few drugs to treat it. Our previous studies demonstrated that the signal integration protein Gab2 is a potential drug target for the prevention and therapy of liver cancer. Here, we screened for and identified two miRNAs that target Gab2 to suppress the proliferation and migration of hepatocellular carcinoma (HCC) cells. First, we predicted Gab2-targeting miRNAs through biological websites, and we selected nine miRNAs that were reported in the literature as being abnormally expressed in liver cancer and fatty liver tissue. Then, we measured the expression of these miRNAs in the hepatic epithelial cell line HL-7702 and the HCC cell line HepG2. The expression levels of miR-9, miR-181a, miR-181c, miR-34a, and miR-134 were high in HL-7702 cells but low in HepG2 cells, and their expression patterns were the opposite of Gab2 in these cells. Furthermore, we transfected miR-9, miR-34a, miR-181a, and miR-181c mimics into HepG2 cells and found that only miR-9 and miR-181a reduced the level of Gab2 proteins. miR-9 also reduced the Gab2 mRNA level, but miR-181a did not affect the Gab2 mRNA levels. Using a miRNA-Gab2 3′UTR binding reporter, we confirmed that miR-9 and miR-181a bind to the Gab2 3′UTR region. Finally, we introduced miR-9 and miR-181a mimics into HepG2 cells and found that cell proliferation and migration were significantly inhibited. In conclusion, we identified two novel miRNAs targeting Gab2 and provided potential drug targets for the prevention and treatment of liver cancer. Full article

The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the Mother’s Curse phenomenon. As mtDNA is inherited from females to all offspring, mutations that are harmful to males tend to accumulate more easily. The Mother’s Curse is associated with various diseases, and has a significant effect on males, in many cases even affecting their reproductive ability. Sometimes, it even leads to reproductive isolation, as in crosses between different populations, the mitochondrial genome cannot cooperate effectively with the nuclear one resulting in a mito-nuclear incompatibility and reduce the fitness of the hybrids. This phenomenon is observed both in the laboratory and in natural populations, and have the potential to influence their evolution and speciation. Therefore, it turns out that the study of mitochondria is an exciting field that finds many applications, including pest control, and it can shed light on the molecular mechanism of several diseases, improving successful diagnosis and therapeutics. Finally, mito-nuclear co-adaptation, paternal leakage, and kin selection are some mechanisms that can mitigate the impact of the Mother’s Curse. Full article

SNPs in ABCA7 confer the largest genetic risk for Alzheimer’s Disease (AD) in African Americans (AA) after APOE ε4. However, the relationship between ABCA7 and cognitive function has not been thoroughly examined. We investigated the effects of five known AD risk SNPs and 72 CpGs in ABCA7, as well as their interactions, on general cognitive function (cognition) in 634 older AA without dementia from Genetic Epidemiology Network of Arteriopathy (GENOA). Using linear mixed models, no SNP or CpG was associated with cognition after multiple testing correction, but five CpGs were nominally associated (p < 0.05). Four SNP-by-CpG interactions were associated with cognition (FDR q < 0.1). Contrast tests show that methylation is associated with cognition in some genotype groups (p < 0.05): a 1% increase at cg00135882 and cg22271697 is associated with a 0.68 SD decrease and 0.14 SD increase in cognition for those with the rs3764647 GG/AG (p = 0.004) and AA (p = 2 × 10⁻⁴) genotypes, respectively. In addition, a 1% increase at cg06169110 and cg17316918 is associated with a 0.37 SD decrease (p = 2 × 10⁻⁴) and 0.33 SD increase (p = 0.004), respectively, in cognition for those with the rs115550680 GG/AG genotype. While AD risk SNPs in ABCA7 were not associated with cognition in this sample, some have interactions with proximal methylation on cognition. Full article

Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs. Full article

Genetic factors can influence the risk of coronary artery disease (CAD) and the survival of patients. Our previous research led to the identification of genetic variants predisposing to CAD in the Polish population. Since many of them affect the clinical phenotype of the disease, the aim of this study was searching for genetic factors potentially influencing survival in patients with CAD. The study included 276 patients hospitalized due to coronary artery disease. The database of medical history and genotypic results of 29 polymorphisms were used. The endpoint was defined as death from cardiovascular causes. Survival was defined as the period from angiographic confirmation of CAD to death from cardiovascular causes. Three of all the analyzed genes were associated with survival. In the case of the AGT (rs699) and ABCA1 (rs2230806) genes polymorphisms, the risk of death was higher in GG homozygotes compared to the A allele carriers in the 10-year period. In the case of the CYBA (rs72811418) gene polymorphism, the effect on mortality was shown in both 5- and 10-year periods. The TA heterozygotes were predisposed to a higher risk of death than the TT homozygotes. Concluding, the AGT, ABCA1, and CYBA genes polymorphisms influence the risk of death in patients with CAD. Full article

The COVID-19 pandemic initiated a race to determine the best measures to control the disease and to save as many people as possible. Efforts to implement social distancing, the use of masks, and massive vaccination programs turned out to be essential in reducing the devastating effects of the pandemic. Nevertheless, the high mutation rates of SARS-CoV-2 challenge the vaccination strategy and maintain the threat of new outbreaks due to the risk of infection surges and even lethal variations able to resist the effects of vaccines and upset the balance. Most of the new therapies tested against SARS-CoV-2 came from already available formulations developed to treat other diseases, so they were not specifically developed for SARS-CoV-2. In parallel, the knowledge produced regarding the molecular mechanisms involved in this disease was vast due to massive efforts worldwide. Taking advantage of such a vast molecular understanding of virus genomes and disease mechanisms, a targeted molecular therapy based on siRNA specifically developed to reach exclusive SARS-CoV-2 genomic sequences was tested in a non-transformed human cell model. Since coronavirus can escape from siRNA by producing siRNA inhibitors, a complex strategy to simultaneously strike both the viral infectious mechanism and the capability of evading siRNA therapy was developed. The combined administration of the chosen produced siRNA proved to be highly effective in successfully reducing viral load and keeping virus replication under control, even after many days of treatment, unlike the combinations of siRNAs lacking this anti-anti-siRNA capability. Additionally, the developed therapy did not harm the normal cells, which was demonstrated because, instead of testing the siRNA in nonhuman cells or in transformed human cells, a non-transformed human thyroid cell was specifically chosen for the experiment. The proposed siRNA combination could reduce the viral load and allow the cellular recovery, presenting a potential innovation for consideration as an additional strategy to counter or cope COVID-19. Full article