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Volume 14
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Genes, Volume 14, Issue 8 (August 2023) – 150 articles

Cover Story (view full-size image): An article by Christen et al. in this issue describes a new hereditary form of cerebellar ataxia in Belgian Shepherds. The study characterizes the clinical and histopathologic phenotype along with the likely causal genetic variant in the RALGAPA1 gene. The results allow us to perform genetic testing to avoid the unintentional breeding of affected offspring. View this paper
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18 pages, 4638 KiB  
Article
HmbC, a Protein of the HMG Family, Participates in the Regulation of Carotenoid Biosynthesis in Fusarium fujikuroi
by Marta Franco-Losilla, Steffen Nordzieke, Ingo Feldmann, M. Carmen Limón and Javier Avalos
Genes 2023, 14(8), 1661; https://doi.org/10.3390/genes14081661 - 21 Aug 2023
Cited by 2 | Viewed by 1546
Abstract
In the fungus Fusarium fujikuroi, carotenoid production is up-regulated by light and down-regulated by the CarS RING finger protein, which modulates the mRNA levels of carotenoid pathway genes (car genes). To identify new potential regulators of car genes, we used a [...] Read more.
In the fungus Fusarium fujikuroi, carotenoid production is up-regulated by light and down-regulated by the CarS RING finger protein, which modulates the mRNA levels of carotenoid pathway genes (car genes). To identify new potential regulators of car genes, we used a biotin-mediated pull-down procedure to detect proteins capable of binding to their promoters. We focused our attention on one of the proteins found in the screening, belonging to the High-Mobility Group (HMG) family that was named HmbC. The deletion of the hmbC gene resulted in increased carotenoid production due to higher mRNA levels of car biosynthetic genes. In addition, the deletion resulted in reduced carS mRNA levels, which could also explain the partial deregulation of the carotenoid pathway. The mutants exhibited other phenotypic traits, such as alterations in development under certain stress conditions, or reduced sensitivity to cell wall degrading enzymes, revealed by less efficient protoplast formation, indicating that HmbC is also involved in other cellular processes. In conclusion, we identified a protein of the HMG family that participates in the regulation of carotenoid biosynthesis. This is probably achieved through an epigenetic mechanism related to chromatin structure, as is frequent in this class of proteins. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2023)
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18 pages, 3099 KiB  
Article
SMRT Sequencing Enables High-Throughput Identification of Novel AAVs from Capsid Shuffling and Directed Evolution
by Widler Casy, Irvin T. Garza, Xin Chen, Thomas Dong, Yuhui Hu, Mohammed Kanchwala, Cynthia B. Trygg, Charles Shyng, Chao Xing, Bruce A. Bunnell, Stephen E. Braun and Steven J. Gray
Genes 2023, 14(8), 1660; https://doi.org/10.3390/genes14081660 - 21 Aug 2023
Cited by 1 | Viewed by 2818
Abstract
The use of AAV capsid libraries coupled with various selection strategies has proven to be a remarkable approach for generating novel AAVs with enhanced and desired features. The inability to reliably sequence the complete capsid gene in a high-throughput manner has been the [...] Read more.
The use of AAV capsid libraries coupled with various selection strategies has proven to be a remarkable approach for generating novel AAVs with enhanced and desired features. The inability to reliably sequence the complete capsid gene in a high-throughput manner has been the bottleneck of capsid engineering. As a result, many library strategies are confined to localized and modest alterations in the capsid, such as peptide insertions or single variable region (VR) alterations. The caveat of short reads by means of next-generation sequencing (NGS) hinders the diversity of capsid library construction, shifting the field away from whole-capsid modifications. We generated AAV capsid shuffled libraries of naturally occurring AAVs and applied directed evolution in both mice and non-human primates (NHPs), with the goal of yielding AAVs that are compatible across both species for translational applications. We recovered DNA from the tissues of injected animal and used single molecule real-time (SMRT) sequencing to identify variants enriched in the central nervous system (CNS). We provide insights and considerations for variant identification by comparing bulk tissue sequencing to that of isolated nuclei. Our work highlights the potential advantages of whole-capsid engineering, as well as indispensable methodological improvements for the analysis of recovered capsids, including the nuclei-enrichment step and SMRT sequencing. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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12 pages, 3365 KiB  
Case Report
A Splicing Variant in RDH8 Is Associated with Autosomal Recessive Stargardt Macular Dystrophy
by Stefania Zampatti, Cristina Peconi, Giulia Calvino, Rosangela Ferese, Stefano Gambardella, Raffaella Cascella, Jacopo Sebastiani, Benedetto Falsini, Andrea Cusumano and Emiliano Giardina
Genes 2023, 14(8), 1659; https://doi.org/10.3390/genes14081659 - 21 Aug 2023
Cited by 2 | Viewed by 1242
Abstract
Stargardt macular dystrophy is a genetic disorder, but in many cases, the causative gene remains unrevealed. Through a combined approach (whole-exome sequencing and phenotype/family-driven filtering algorithm) and a multilevel validation (international database searching, prediction scores calculation, splicing analysis assay, segregation analyses), a biallelic [...] Read more.
Stargardt macular dystrophy is a genetic disorder, but in many cases, the causative gene remains unrevealed. Through a combined approach (whole-exome sequencing and phenotype/family-driven filtering algorithm) and a multilevel validation (international database searching, prediction scores calculation, splicing analysis assay, segregation analyses), a biallelic mutation in the RDH8 gene was identified to be responsible for Stargardt macular dystrophy in a consanguineous Italian family. This paper is a report on the first family in which a biallelic deleterious mutation in RDH8 is detected. The disease phenotype is consistent with the expected phenotype hypothesized in previous studies on murine models. The application of the combined approach to genetic data and the multilevel validation allowed the identification of a splicing mutation in a gene that has never been reported before in human disorders. Full article
(This article belongs to the Collection Genetics and Genomics of Rare Disorders)
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20 pages, 1128 KiB  
Review
Neuroinflammatory Pathways in the ALS-FTD Continuum: A Focus on Genetic Variants
by Fabiola De Marchi, Giacomo Tondo, Lucia Corrado, Federico Menegon, Davide Aprile, Matteo Anselmi, Sandra D’Alfonso, Cristoforo Comi and Letizia Mazzini
Genes 2023, 14(8), 1658; https://doi.org/10.3390/genes14081658 - 21 Aug 2023
Cited by 6 | Viewed by 4132
Abstract
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FDT) are progressive neurodegenerative disorders that, in several cases, overlap in clinical presentation, and genetic and pathological disease mechanisms. About 10–15% of ALS cases and up to 40% of FTD are familial, usually with dominant traits. [...] Read more.
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FDT) are progressive neurodegenerative disorders that, in several cases, overlap in clinical presentation, and genetic and pathological disease mechanisms. About 10–15% of ALS cases and up to 40% of FTD are familial, usually with dominant traits. ALS and FTD, in several cases, share common gene mutations, such as in C9ORF72, TARDBP, SQSTM-1, FUS, VCP, CHCHD10, and TBK-1. Also, several mechanisms are involved in ALS and FTD pathogenesis, such as protein misfolding, oxidative stress, and impaired axonal transport. In addition, neuroinflammation and neuroinflammatory cells, such as astrocytes, oligodendrocytes, microglia, and lymphocytes and, overall, the cellular microenvironment, have been proposed as pivotal players in the pathogenesis the ALS-FTD spectrum disorders. This review overviews the current evidence regarding neuroinflammatory markers in the ALS/FTD continuum, focusing on the neuroinflammatory pathways involved in the genetic cases, moving from post-mortem reports to in vivo biofluid and neuroimaging data. We further discuss the potential link between genetic and autoimmune disorders and potential therapeutic implications. Full article
(This article belongs to the Special Issue Research Strategies to Unveil the Genetic and Molecular Basis of ALS)
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47 pages, 853 KiB  
Article
Genomic Distribution of ushA-like Genes in Bacteria: Comparison to cpdB-like Genes
by João Meireles Ribeiro and José Carlos Cameselle
Genes 2023, 14(8), 1657; https://doi.org/10.3390/genes14081657 - 20 Aug 2023
Viewed by 1199
Abstract
UshA and CpdB are nucleotidases of the periplasm of several Gram-negative bacteria, while several Gram-positives contain cell wall-bound variants. UshA is a 5′-nucleotidase, a UDP-sugar hydrolase, and a CDP-alcohol hydrolase. CpdB acts as a 3′-nucleotidase and as a phosphodiesterase of 2′,3′-cyclic nucleotides and [...] Read more.
UshA and CpdB are nucleotidases of the periplasm of several Gram-negative bacteria, while several Gram-positives contain cell wall-bound variants. UshA is a 5′-nucleotidase, a UDP-sugar hydrolase, and a CDP-alcohol hydrolase. CpdB acts as a 3′-nucleotidase and as a phosphodiesterase of 2′,3′-cyclic nucleotides and 3′,5′-linear and cyclic dinucleotides. Both proteins are pro-virulent for the pathogens producing them and facilitate escape from the innate immunity of the infected host. Recently, the genomic distribution of cpdB-like genes in Bacteria was found to be non-homogeneous among different taxa, and differences occur within single taxa, even at species level. Similitudes and differences between UshA-like and CpdB-like proteins prompted parallel analysis of their genomic distributions in Bacteria. The presence of ushA-like and cpdB-like genes was tested by TBlastN analysis using seven protein probes to query the NCBI Complete Genomes Database. It is concluded that the distribution of ushA-like genes, like that of cpdB-like genes, is non-homogeneous. There is a partial correlation between both gene kinds: in some taxa, both are present or absent, while in others, only one is present. The result is an extensive catalog of the genomic distribution of these genes at different levels, from phylum to species, constituting a starting point for research using other in silico or experimental approaches. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2023)
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15 pages, 2823 KiB  
Review
Diverse Clinical Phenotypes of CASK-Related Disorders and Multiple Functional Domains of CASK Protein
by Takuma Mori, Mengyun Zhou and Katsuhiko Tabuchi
Genes 2023, 14(8), 1656; https://doi.org/10.3390/genes14081656 - 20 Aug 2023
Cited by 5 | Viewed by 2550
Abstract
CASK-related disorders are a form of rare X-linked neurological diseases and most of the patients are females. They are characterized by several symptoms, including microcephaly with pontine and cerebellar hypoplasia (MICPCH), epilepsy, congenital nystagmus, and neurodevelopmental disorders. Whole-genome sequencing has identified various [...] Read more.
CASK-related disorders are a form of rare X-linked neurological diseases and most of the patients are females. They are characterized by several symptoms, including microcephaly with pontine and cerebellar hypoplasia (MICPCH), epilepsy, congenital nystagmus, and neurodevelopmental disorders. Whole-genome sequencing has identified various mutations, including nonsense and missense mutations, from patients with CASK-related disorders, revealing correlations between specific mutations and clinical phenotypes. Notably, missense mutations associated with epilepsy and intellectual disability were found throughout the whole region of the CASK protein, while missense mutations related to microcephaly and MICPCH were restricted in certain domains. To investigate the pathophysiology of CASK-related disorders, research groups have employed diverse methods, including the generation of CASK knockout mice and the supplementation of CASK to rescue the phenotypes. These approaches have yielded valuable insights into the identification of functional domains of the CASK protein associated with a specific phenotype. Additionally, recent advancements in the AI-based prediction of protein structure, such as AlphaFold2, and the application of genome-editing techniques to generate CASK mutant mice carrying missense mutations from patients with CASK-related disorders, allow us to understand the pathophysiology of CASK-related disorders in more depth and to develop novel therapeutic methods for the fundamental treatment of CASK-related disorders. Full article
(This article belongs to the Special Issue Animals Models in Diseases Genetics)
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16 pages, 1765 KiB  
Systematic Review
PSTPIP1-Associated Myeloid-Related Proteinemia Inflammatory (PAMI) Syndrome: A Systematic Review
by Manel Mejbri, Raffaele Renella, Fabio Candotti, Cecile Jaques, Dirk Holzinger, Michael Hofer and Katerina Theodoropoulou
Genes 2023, 14(8), 1655; https://doi.org/10.3390/genes14081655 - 19 Aug 2023
Cited by 1 | Viewed by 2497
Abstract
PSTPIP1 (proline-serine-threonine phosphatase-interactive protein 1)-associated myeloid-related proteinemia inflammatory (PAMI) syndrome, previously known as Hyperzincemia/Hypercalprotectinemia (Hz/Hc) syndrome, is a recently described, rare auto-inflammatory disorder caused by specific deleterious variants in the PSTPIP1 gene (p.E250K and p.E257K). The disease is characterized by chronic systemic inflammation, [...] Read more.
PSTPIP1 (proline-serine-threonine phosphatase-interactive protein 1)-associated myeloid-related proteinemia inflammatory (PAMI) syndrome, previously known as Hyperzincemia/Hypercalprotectinemia (Hz/Hc) syndrome, is a recently described, rare auto-inflammatory disorder caused by specific deleterious variants in the PSTPIP1 gene (p.E250K and p.E257K). The disease is characterized by chronic systemic inflammation, cutaneous and osteoarticular manifestations, hepatosplenomegaly, anemia, and neutropenia. Increased blood levels of MRP 8/14 and zinc distinguish this condition from other PSTPIP1-associated inflammatory diseases (PAID). The aim of this systematic review is to provide a comprehensive overview of the disease phenotype, course, treatment, and outcome based on reported cases. This systematic review adheres to the PRISMA guidelines (2020) for reporting. A literature search was performed in Embase, Medline, and Web of Science on 13 October 2022. The quality of the case reports and case series was assessed using the JBI checklists. Out of the 43 included patients with PAMI syndrome, there were 24 females and 19 males. The median age at onset was 3.9 years. The main clinical manifestations included anemia (100%), neutropenia (98%), cutaneous manifestations (74%), osteoarticular manifestations (72%), splenomegaly (70%), growth failure (57%), fever (51%), hepatomegaly (56%), and lymphadenopathy (39%). Systemic inflammation was described in all patients. Marked elevation of zinc and MRP 8/14 blood levels were observed in all tested patients. Response to treatment varied and no consistently effective therapy was identified. The most common therapeutic options were corticosteroids (N = 30), anakinra (N = 13), cyclosporine A (N = 11), canakinumab (N = 6), and anti-TNF (N = 14). Hematopoietic stem cell transplantation has been recently reported to be successful in five patients. Our review highlights the key characteristics of PAMI syndrome and the importance of considering this disease in the differential diagnosis of patients presenting with early-onset systemic inflammation and cytopenia. Full article
(This article belongs to the Special Issue Autoimmunity and Autoinflammatory Genetic Syndromes)
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20 pages, 3403 KiB  
Article
Finding an Appropriate Mouse Model to Study the Impact of a Treatment for Friedreich Ataxia on the Behavioral Phenotype
by Camille Bouchard, Catherine Gérard, Solange Gni-fiene Yanyabé, Nathalie Majeau, Malek Aloui, Gabrielle Buisson, Pouiré Yameogo, Vanessa Couture and Jacques P. Tremblay
Genes 2023, 14(8), 1654; https://doi.org/10.3390/genes14081654 - 19 Aug 2023
Cited by 2 | Viewed by 2488
Abstract
Friedreich ataxia (FRDA) is a progressive neurodegenerative disease caused by a GAA repeat in the intron 1 of the frataxin gene (FXN) leading to a lower expression of the frataxin protein. The YG8sR mice are Knock-Out (KO) for their murine frataxin gene but [...] Read more.
Friedreich ataxia (FRDA) is a progressive neurodegenerative disease caused by a GAA repeat in the intron 1 of the frataxin gene (FXN) leading to a lower expression of the frataxin protein. The YG8sR mice are Knock-Out (KO) for their murine frataxin gene but contain a human frataxin transgene derived from an FRDA patient with 300 GAA repeats. These mice are used as a FRDA model but even with a low frataxin concentration, their phenotype is mild. We aimed to find an optimized mouse model with a phenotype comparable to the human patients to study the impact of therapy on the phenotype. We compared two mouse models: the YG8sR injected with an AAV. PHP.B coding for a shRNA targeting the human frataxin gene and the YG8-800, a new mouse model with a human transgene containing 800 GAA repeats. Both mouse models were compared to Y47R mice containing nine GAA repeats that were considered healthy mice. Behavior tests (parallel rod floor apparatus, hanging test, inverted T beam, and notched beam test) were carried out from 2 to 11 months and significant differences were noticed for both YG8sR mice injected with an anti-FXN shRNA and the YG8-800 mice compared to healthy mice. In conclusion, YG8sR mice have a slight phenotype, and injecting them with an AAV-PHP.B expressing an shRNA targeting frataxin does increase their phenotype. The YG8-800 mice have a phenotype comparable to the human ataxic phenotype. Full article
(This article belongs to the Special Issue Study on Genotypes and Phenotypes of Neurodegenerative Diseases)
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24 pages, 1664 KiB  
Review
Changes in m6A in Steatotic Liver Disease
by Belinda J. Petri, Matthew C. Cave and Carolyn M. Klinge
Genes 2023, 14(8), 1653; https://doi.org/10.3390/genes14081653 - 19 Aug 2023
Cited by 5 | Viewed by 2868
Abstract
Fatty liver disease is one of the major causes of morbidity and mortality worldwide. Fatty liver includes non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), now replaced by a consensus group as metabolic dysfunction-associated steatotic liver disease (MASLD). While excess nutrition and [...] Read more.
Fatty liver disease is one of the major causes of morbidity and mortality worldwide. Fatty liver includes non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), now replaced by a consensus group as metabolic dysfunction-associated steatotic liver disease (MASLD). While excess nutrition and obesity are major contributors to fatty liver, the underlying mechanisms remain largely unknown and therapeutic interventions are limited. Reversible chemical modifications in RNA are newly recognized critical regulators controlling post-transcriptional gene expression. Among these modifications, N6-methyladenosine (m6A) is the most abundant and regulates transcript abundance in fatty liver disease. Modulation of m6A by readers, writers, and erasers (RWE) impacts mRNA processing, translation, nuclear export, localization, and degradation. While many studies focus on m6A RWE expression in human liver pathologies, limitations of technology and bioinformatic methods to detect m6A present challenges in understanding the epitranscriptomic mechanisms driving fatty liver disease progression. In this review, we summarize the RWE of m6A and current methods of detecting m6A in specific genes associated with fatty liver disease. Full article
(This article belongs to the Section RNA)
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17 pages, 2457 KiB  
Article
Novel α-1,3-Glucosyltransferase Variants and Their Broad Clinical Polycystic Liver Disease Spectrum
by Melissa M. Boerrigter, René H. M. te Morsche, Hanka Venselaar, Nikki Pastoors, Anja M. Geerts, Anne Hoorens and Joost P. H. Drenth
Genes 2023, 14(8), 1652; https://doi.org/10.3390/genes14081652 - 19 Aug 2023
Cited by 1 | Viewed by 1353
Abstract
Protein-truncating variants in α-1,3-glucosyltransferase (ALG8) are a risk factor for a mild cystic kidney disease phenotype. The association between these variants and liver cysts is limited. We aim to identify pathogenic ALG8 variants in our cohort of autosomal dominant polycystic liver [...] Read more.
Protein-truncating variants in α-1,3-glucosyltransferase (ALG8) are a risk factor for a mild cystic kidney disease phenotype. The association between these variants and liver cysts is limited. We aim to identify pathogenic ALG8 variants in our cohort of autosomal dominant polycystic liver disease (ADPLD) individuals. In order to fine-map the phenotypical spectrum of pathogenic ALG8 variant carriers, we performed targeted ALG8 screening in 478 ADPLD singletons, and exome sequencing in 48 singletons and 4 patients from two large ADPLD families. Eight novel and one previously reported pathogenic variant in ALG8 were discovered in sixteen patients. The ALG8 clinical phenotype ranges from mild to severe polycystic liver disease, and from innumerable small to multiple large hepatic cysts. The presence of <5 renal cysts that do not affect renal function is common in this population. Three-dimensional homology modeling demonstrated that six variants cause a truncated ALG8 protein with abnormal functioning, and one variant is predicted to destabilize ALG8. For the seventh variant, immunostaining of the liver tissue showed a complete loss of ALG8 in the cystic cells. ALG8-associated ADPLD has a broad clinical spectrum, including the possibility of developing a small number of renal cysts. This broadens the ADPLD genotype–phenotype spectrum and narrows the gap between liver-specific ADPLD and kidney-specific ADPKD. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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11 pages, 736 KiB  
Case Report
The Potential Usefulness of the Expanded Carrier Screening to Identify Hereditary Genetic Diseases: A Case Report from Real-World Data
by Iolanda Veneruso, Annaluisa Ranieri, Noemi Falcone, Lorella Tripodi, Carmela Scarano, Ilaria La Monica, Lucio Pastore, Barbara Lombardo and Valeria D’Argenio
Genes 2023, 14(8), 1651; https://doi.org/10.3390/genes14081651 - 19 Aug 2023
Viewed by 1814
Abstract
Expanded carrier screening (ECS) means a comprehensive genetic analysis to evaluate an individual’s carrier status. ECS is becoming more frequently used, thanks to the availability of techniques such as next generation sequencing (NGS) and array comparative genomic hybridization (aCGH), allowing for extensive genome-scale [...] Read more.
Expanded carrier screening (ECS) means a comprehensive genetic analysis to evaluate an individual’s carrier status. ECS is becoming more frequently used, thanks to the availability of techniques such as next generation sequencing (NGS) and array comparative genomic hybridization (aCGH), allowing for extensive genome-scale analyses. Here, we report the case of a couple who underwent ECS for a case of autism spectrum disorder in the male partner family. aCGH and whole-exome sequencing (WES) were performed in the couple. aCGH analysis identified in the female partner two deletions involving genes associated to behavioral and neurodevelopment disorders. No clinically relevant alterations were identified in the husband. Interestingly, WES analysis identified in the male partner a pathogenic variant in the LPL gene that is emerging as a novel candidate gene for autism. This case shows that ECS may be useful in clinical contexts, especially when both the partners are analyzed before conception, thus allowing the estimation of their risk to transmit an inherited condition. On the other side, there are several concerns related to possible incidental findings and difficult-to-interpret results. Once these limits are defined by the establishment of specific guidelines, ECS may have a greater diffusion. Full article
(This article belongs to the Special Issue Genetics and Genomics of Prenatal Testing)
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15 pages, 2855 KiB  
Article
SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian Approach
by Beatriz Soriano, Ahmed Ibrahem Hafez, Fernando Naya-Català, Federico Moroni, Roxana Andreea Moldovan, Socorro Toxqui-Rodríguez, María Carla Piazzon, Vicente Arnau, Carlos Llorens and Jaume Pérez-Sánchez
Genes 2023, 14(8), 1650; https://doi.org/10.3390/genes14081650 - 19 Aug 2023
Cited by 1 | Viewed by 2423
Abstract
Gut microbiomes of fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these [...] Read more.
Gut microbiomes of fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to (i) infer information of how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and (ii) predict how the diversity and functional profile of that microbiome would change under other variable conditions. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of Bayesian network scenarios created by SAMBA using data from a microbial synthetic community, and the pan-microbiome of gilthead sea bream (Sparus aurata) in different feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems as it can be used for modelling microbiome–host network relationships of any vertebrate organism, including humans, in any system and/or ecosystem. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants and Animals)
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21 pages, 6821 KiB  
Article
Analyzes In Silico Indicate the lncRNAs MIR31HG and LINC00939 as Possible Epigenetic Inhibitors of the Osteogenic Differentiation in PDLCs
by Rogério S. Ferreira, Rahyza I. F. Assis, Francesca Racca, Ana Carolina Bontempi, Rodrigo A. da Silva, Malgorzata Wiench and Denise C. Andia
Genes 2023, 14(8), 1649; https://doi.org/10.3390/genes14081649 - 18 Aug 2023
Cited by 1 | Viewed by 1710
Abstract
Chromatin conformation, DNA methylation pattern, transcriptional profile, and non-coding RNAs (ncRNAs) interactions constitute an epigenetic pattern that influences the cellular phenotypic commitment and impacts the clinical outcomes in regenerative therapies. Here, we investigated the epigenetic landscape of the SP7 transcriptor factor (SP7 [...] Read more.
Chromatin conformation, DNA methylation pattern, transcriptional profile, and non-coding RNAs (ncRNAs) interactions constitute an epigenetic pattern that influences the cellular phenotypic commitment and impacts the clinical outcomes in regenerative therapies. Here, we investigated the epigenetic landscape of the SP7 transcriptor factor (SP7) and Distal-Less Homeobox 4 (DLX4) osteoblastic transcription factors (TFs), in human periodontal ligament mesenchymal cells (PDLCs) with low (l-PDLCs) and high (h-PDLCs) osteogenic potential. Chromatin accessibility (ATAC-seq), genome DNA methylation (Methylome), and RNA sequencing (RNA-seq) assays were performed in l- and h-PDLCs, cultured at 10 days in non-induced (DMEM) and osteogenic (OM) medium in vitro. Data were processed in HOMER, Genome Studio, and edgeR programs, and metadata was analyzed by online bioinformatics tools and in R and Python environments. ATAC-seq analyses showed the TFs genomic regions are more accessible in l-PDLCs than in h-PDLCs. In Methylome analyses, the TFs presented similar average methylation intensities (AMIs), without differently methylated probes (DMPs) between l- and h-PDLCs; in addition, there were no differences in the expression profiles of TFs signaling pathways. Interestingly, we identified the long non-coding RNAs (lncRNAs), MIR31HG and LINC00939, as upregulated in l-PDLCs, in both DMEM and OM. In the following analysis, the web-based prediction tool LncRRIsearch predicted RNA:RNA base-pairing interactions between SP7, DLX4, MIR31HG, and LINC00939 transcripts. The machine learning program TriplexFPP predicted DNA:RNA triplex-forming potential for the SP7 DNA site and for one of the LINC00939 transcripts (ENST00000502479). PCR data confirmed the upregulation of MIR31HG and LINC00939 transcripts in l-PDLCs (× h-PDLCs) in both DMEM and OM (p < 0.05); conversely, SP7 and DLX4 were downregulated, confirming those results observed in the RNA-Seq analysis. Together, these results indicate the lncRNAs MIR31HG and LINC00939 as possible epigenetic inhibitors of the osteogenic differentiation in PDLCs by (post)transcriptional and translational repression of the SP7 and DLX4 TFs. Full article
(This article belongs to the Special Issue Epigenetics in Human Development and Disease)
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12 pages, 2612 KiB  
Article
Combine with RNA-seq Reveals the Effect of Melatonin in the Synthesis of Melanin in Primary Melanocytes of Silky Fowls Black-Bone Chicken
by Ting Yang, Lingling Qiu, Shihao Chen, Zhixiu Wang, Yong Jiang, Hao Bai, Yulin Bi and Guobin Chang
Genes 2023, 14(8), 1648; https://doi.org/10.3390/genes14081648 - 18 Aug 2023
Cited by 3 | Viewed by 1869
Abstract
(1) Background: It was found that the melanin of black-bone chicken has various effects such as scavenging DPPH free radicals and anti-oxidation, and the synthesis of melanin is affected by various factors including hormones. In addition, several studies have found that melatonin affects [...] Read more.
(1) Background: It was found that the melanin of black-bone chicken has various effects such as scavenging DPPH free radicals and anti-oxidation, and the synthesis of melanin is affected by various factors including hormones. In addition, several studies have found that melatonin affects the melanoma cell synthesis of melanin, which has not been reported in chicken primary melanocytes; so, relevant studies were conducted. (2) Methods: In this study, chicken primary melanocytes were isolated and characterized, and then melanocytes were treated with different concentrations of melatonin to investigate the effects of melatonin on melanin synthesis in chicken melanocytes in terms of melanin synthesis-related genes, melanin content, and tyrosinase activity, and combined with RNA seq to detect the change in gene expression level of chicken melanocytes after melatonin treatment. (3) Results: We isolated and characterized primary melanocytes, and indirect immunofluorescence assay results showed positive melanocyte marker genes. RT-qPCR results showed that melatonin decreased the expression of melanin synthesis-related genes. In addition, melatonin reduced the melanin content and decreased the tyrosinase activity of melanocytes in the treated group. A total of 1703 differentially expressed genes were screened by RNA-seq, and in addition, in the KEGG results, the signaling pathway associated with melanin synthesis, and the mTOR signaling pathway were enriched. (4) Conclusions: Melatonin could decrease the synthesis of melanin in chicken primary melanocytes. Full article
(This article belongs to the Special Issue Poultry Genetics and Genomics)
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19 pages, 4914 KiB  
Article
StrainIQ: A Novel n-Gram-Based Method for Taxonomic Profiling of Human Microbiota at the Strain Level
by Sanjit Pandey, Nagavardhini Avuthu and Chittibabu Guda
Genes 2023, 14(8), 1647; https://doi.org/10.3390/genes14081647 - 18 Aug 2023
Cited by 1 | Viewed by 1439
Abstract
The emergence of next-generation sequencing (NGS) technology has greatly influenced microbiome research and led to the development of novel bioinformatics tools to deeply analyze metagenomics datasets. Identifying strain-level variations in microbial communities is important to understanding the onset and progression of diseases, host–pathogen [...] Read more.
The emergence of next-generation sequencing (NGS) technology has greatly influenced microbiome research and led to the development of novel bioinformatics tools to deeply analyze metagenomics datasets. Identifying strain-level variations in microbial communities is important to understanding the onset and progression of diseases, host–pathogen interrelationships, and drug resistance, in addition to designing new therapeutic regimens. In this study, we developed a novel tool called StrainIQ (strain identification and quantification) based on a new n-gram-based (series of n number of adjacent nucleotides in the DNA sequence) algorithm for predicting and quantifying strain-level taxa from whole-genome metagenomic sequencing data. We thoroughly evaluated our method using simulated and mock metagenomic datasets and compared its performance with existing methods. On average, it showed 85.8% sensitivity and 78.2% specificity on simulated datasets. It also showed higher specificity and sensitivity using n-gram models built from reduced reference genomes and on models with lower coverage sequencing data. It outperforms alternative approaches in genus- and strain-level prediction and strain abundance estimation. Overall, the results show that StrainIQ achieves high accuracy by implementing customized model-building and is an efficient tool for site-specific microbial community profiling. Full article
(This article belongs to the Section Bioinformatics)
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14 pages, 1002 KiB  
Review
Molecular Regulatory Mechanisms in Chicken Feather Follicle Morphogenesis
by Gaige Ji, Ming Zhang, Yunjie Tu, Yifan Liu, Yanju Shan, Xiaojun Ju, Jianmin Zou, Jingting Shu, Zhongwei Sheng and Hua Li
Genes 2023, 14(8), 1646; https://doi.org/10.3390/genes14081646 - 18 Aug 2023
Cited by 5 | Viewed by 2854
Abstract
In China, the sale of freshly slaughtered chickens is becoming increasingly popular in comparison with that of live chickens, and due to this emerging trend, the skin and feather follicle traits of yellow-feathered broilers have attracted a great deal of research attention. The [...] Read more.
In China, the sale of freshly slaughtered chickens is becoming increasingly popular in comparison with that of live chickens, and due to this emerging trend, the skin and feather follicle traits of yellow-feathered broilers have attracted a great deal of research attention. The feather follicle originates from the interaction between the epidermis and dermis in the early embryonic stage. Feather follicle morphogenesis is regulated by the Wnt, ectodysplasin (Eda), epidermal growth factor (EGF), fibroblast growth factor (FGF), bone morphogenetic protein (BMP), sonic hedgehog (Shh), Notch, and other signaling pathways that exist in epithelial and mesenchymal cells. The Wnt pathway is essential for feather follicle and feather morphogenesis. Eda interacts with Wnt to induce FGF expression, which attracts mesenchymal cell movement and aggregates to form feather follicle primordia. BMP acts as an inhibitor of the above signaling pathways to limit the size of the feather tract and distance between neighboring feather primordia in a dose-dependent manner. The Notch/Delta pathway can interact with the FGF pathway to promote feather bud formation. While not a part of the early morphogenesis of feather follicles, Shh and BMP signaling are involved in late feather branching. This review summarizes the roles of miRNAs/lncRNA in the regulation of feather follicle and feather growth and development and suggests topics that need to be solved in a future study. This review focuses on the regulatory mechanisms involved in feather follicle morphogenesis and analyzes the impact of SNP sites on feather follicle traits in poultry. This work may help us to understand the molecular regulatory networks influencing feather follicle growth and provide basic data for poultry carcass quality. Full article
(This article belongs to the Special Issue Advances in Poultry Genetics and Breeding)
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13 pages, 1717 KiB  
Article
NuMY—A qPCR Assay Simultaneously Targeting Human Autosomal, Y-Chromosomal, and Mitochondrial DNA
by Catarina Xavier, Charlotte Sutter, Christina Amory, Harald Niederstätter and Walther Parson
Genes 2023, 14(8), 1645; https://doi.org/10.3390/genes14081645 - 18 Aug 2023
Cited by 1 | Viewed by 1973
Abstract
The accurate quantification of DNA in forensic samples is of utmost importance. These samples are often present in limited amounts; therefore, it is indicated to use the appropriate analysis route with the optimum DNA amount (when possible). Also, DNA quantification can inform about [...] Read more.
The accurate quantification of DNA in forensic samples is of utmost importance. These samples are often present in limited amounts; therefore, it is indicated to use the appropriate analysis route with the optimum DNA amount (when possible). Also, DNA quantification can inform about the degradation stage and therefore support the decision on which downstream genotyping method to use. Consequently, DNA quantification aids in getting the best possible results from a forensic sample, considering both its DNA quantity and quality limitations. Here, we introduce NuMY, a new quantitative real-time PCR (qPCR) method for the parallel quantification of human nuclear (n) and mitochondrial (mt) DNA, assessing the male portion in mixtures of both sexes and testing for possible PCR inhibition. NuMY is based on previous work and follows the MIQE guidelines whenever applicable. Although quantification of nuclear (n)DNA by simultaneously analyzing autosomal and male-specific targets is available in commercial qPCR kits, tools that include the quantification of mtDNA are sparse. The quantification of mtDNA has proven relevant for samples with low nDNA content when conventional DNA fingerprinting techniques cannot be followed. Furthermore, the development and use of new massively parallel sequencing assays that combine multiple marker types, i.e., autosomal, Y-chromosomal, and mtDNA, can be optimized when precisely knowing the amount of each DNA component present in the input sample. For high-quality DNA extracts, NuMY provided nDNA results comparable to those of another quantification technique and has also proven to be a reliable tool for challenging, forensically relevant samples such as mixtures, inhibited, and naturally degraded samples. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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16 pages, 1025 KiB  
Article
Polymorphisms in Glutathione S-Transferase (GST) Genes Modify the Effect of Exposure to Maternal Smoking Metabolites in Pregnancy and Offspring DNA Methylation
by Parnian Kheirkhah Rahimabad, A. Daniel Jones, Hongmei Zhang, Su Chen, Yu Jiang, Susan Ewart, John W. Holloway, Hasan Arshad, Shakiba Eslamimehr, Robert Bruce and Wilfried Karmaus
Genes 2023, 14(8), 1644; https://doi.org/10.3390/genes14081644 - 18 Aug 2023
Viewed by 1490
Abstract
Maternal smoking in pregnancy (MSP) affects the offspring’s DNA methylation (DNAm). There is a lack of knowledge regarding individual differences in susceptibility to exposure to MSP. Glutathione S-transferase (GST) genes are involved in protection against harmful oxidants such as those found [...] Read more.
Maternal smoking in pregnancy (MSP) affects the offspring’s DNA methylation (DNAm). There is a lack of knowledge regarding individual differences in susceptibility to exposure to MSP. Glutathione S-transferase (GST) genes are involved in protection against harmful oxidants such as those found in cigarette smoke. This study aimed to test whether polymorphisms in GST genes influence the effect of MSP on offspring DNAm. Using data from the Isle of Wight birth cohort, we assessed the association of MSP and offspring DNAm in 493 mother-child dyads (251 male, 242 female) with the effect-modifying role of GST gene polymorphism (at rs506008, rs574344, rs12736389, rs3768490, rs1537234, and rs1695). MSP was assessed by levels of nicotine and its downstream metabolites (cotinine, norcotinine, and hydroxycotinine) in maternal sera. In males, associations of hydroxycotinine with DNAm at cg18473733, cg25949550, cg11647108, and cg01952185 and norcotinine with DNAm at cg09935388 were modified by GST gene polymorphisms (p-values < 0.05). In females, associations of hydroxycotinine with DNAm at cg12160087 and norcotinine with DNAm at cg18473733 were modified by GST gene polymorphisms (p-values < 0.05). Our study emphasizes the role of genetic polymorphism in GST genes in DNAm’s susceptibility to MSP. Full article
(This article belongs to the Special Issue Feature Papers in Genes & Environments)
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26 pages, 468 KiB  
Review
Nucleic Acids Persistence—Benefits and Limitations in Forensic Genetics
by Małgorzata Żarczyńska, Piotr Żarczyński and Marcin Tomsia
Genes 2023, 14(8), 1643; https://doi.org/10.3390/genes14081643 - 18 Aug 2023
Cited by 2 | Viewed by 3044
Abstract
The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to [...] Read more.
The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
15 pages, 1384 KiB  
Review
Role of Actin Dynamics and GhACTIN1 Gene in Cotton Fiber Development: A Prototypical Cell for Study
by Adnan Iqbal, Sibgha Aslam, Mukhtar Ahmed, Fahad Khan, Qurban Ali and Shiming Han
Genes 2023, 14(8), 1642; https://doi.org/10.3390/genes14081642 - 18 Aug 2023
Cited by 2 | Viewed by 2048
Abstract
Cotton crop is considered valuable for its fiber and seed oil. Cotton fiber is a single-celled outgrowth from the ovule epidermis, and it is a very dynamic cell for study. It has four distinct but overlapping developmental stages: initiation, elongation, secondary cell wall [...] Read more.
Cotton crop is considered valuable for its fiber and seed oil. Cotton fiber is a single-celled outgrowth from the ovule epidermis, and it is a very dynamic cell for study. It has four distinct but overlapping developmental stages: initiation, elongation, secondary cell wall synthesis, and maturation. Among the various qualitative characteristics of cotton fiber, the important ones are the cotton fiber staple length, tensile strength, micronaire values, and fiber maturity. Actin dynamics are known to play an important role in fiber elongation and maturation. The current review gives an insight into the cotton fiber developmental stages, the qualitative traits associated with cotton fiber, and the set of genes involved in regulating these developmental stages and fiber traits. This review also highlights some prospects for how biotechnological approaches can improve cotton fiber quality. Full article
(This article belongs to the Special Issue Plant Breeding: Molecular Genetics, Challenges, Opportunities and Future Perspectives)
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13 pages, 2460 KiB  
Article
SGCD Missense Variant in a Lagotto Romagnolo Dog with Autosomal Recessively Inherited Limb-Girdle Muscular Dystrophy
by Barbara Brunetti, Barbara Bacci, Jessica Maria Abbate, Giorgia Tura, Orlando Paciello, Emanuela Vaccaro, Francesco Prisco, Gualtiero Gandini, Samuel Okonji, Andrea di Paola, Anna Letko, Cord Drögemüller, Vidhya Jagannathan, Maria Elena Turba, Tolulope Grace Ogundipe, Luca Lorenzini, Marco Rosati, Dimitra Psalla, Tosso Leeb and Michaela Drögemüller
Genes 2023, 14(8), 1641; https://doi.org/10.3390/genes14081641 - 18 Aug 2023
Cited by 1 | Viewed by 1690
Abstract
An 8-month-old female Lagotto Romagnolo dog was presented for a 1-month history of an initial severe reluctance to move, rapidly progressing to a marked stiff gait and progressive muscular weakness and evolving to tetraparesis, which persuaded the owner to request euthanasia. A primary [...] Read more.
An 8-month-old female Lagotto Romagnolo dog was presented for a 1-month history of an initial severe reluctance to move, rapidly progressing to a marked stiff gait and progressive muscular weakness and evolving to tetraparesis, which persuaded the owner to request euthanasia. A primary muscle pathology was supported by necropsy and histopathological findings. Macroscopically, the muscles were moderately atrophic, except for the diaphragm and the neck muscles, which were markedly thickened. Histologically, all the skeletal muscles examined showed atrophy, hypertrophy, necrosis with calcification of the fibers, and mild fibrosis and inflammation. On immunohistochemistry, all three dystrophin domains and sarcoglycan proteins were absent. On Western blot analysis, no band was present for delta sarcoglycan. We sequenced the genome of the affected dog and compared the data to more than 900 control genomes of different dog breeds. Genetic analysis revealed a homozygous private protein-changing variant in the SGCD gene encoding delta- sarcoglycan in the affected dog. The variant was predicted to induce a SGCD:p.(Leu242Pro) change in the protein. In silico tools predicted the change to be deleterious. Other 770 Lagotto Romagnolo dogs were genotyped for the variant and all found to be homozygous wild type. Based on current knowledge of gene function in other mammalian species, including humans, hamsters, and dogs, we propose the SGCD missense variant as the causative variant of the observed form of muscular dystrophy in the index case. The absence of the variant allele in the Lagotto Romagnolo breeding population indicates a rare allele that has appeared recently. Full article
(This article belongs to the Special Issue Advances in Canine Genetics)
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12 pages, 1825 KiB  
Article
Transcriptomic Analysis of Tobacco Plants in Response to Whitefly Infection
by Xin Wang, Zhuang-Xin Ye, Yi-Zhe Wang, Xiao-Jing Wang, Jian-Ping Chen and Hai-Jian Huang
Genes 2023, 14(8), 1640; https://doi.org/10.3390/genes14081640 - 18 Aug 2023
Cited by 3 | Viewed by 1639
Abstract
The whitefly Bemisia tabaci is one of the most destructive pests worldwide, and causes tremendous economic losses. Tobacco Nicotiana tabacum serves as a model organism for studying fundamental biological processes and is severely damaged by whiteflies. Hitherto, our knowledge of how tobacco perceives [...] Read more.
The whitefly Bemisia tabaci is one of the most destructive pests worldwide, and causes tremendous economic losses. Tobacco Nicotiana tabacum serves as a model organism for studying fundamental biological processes and is severely damaged by whiteflies. Hitherto, our knowledge of how tobacco perceives and defends itself against whiteflies has been scare. In this study, we analyze the gene expression patterns of tobacco in response to whitefly infestation. A total of 244 and 2417 differentially expressed genes (DEGs) were identified at 12 h and 24 h post whitefly infestation, respectively. Enrichment analysis demonstrates that whitefly infestation activates plant defense at both time points, with genes involved in plant pattern recognition, transcription factors, and hormonal regulation significantly upregulated. Notably, defense genes are more intensely upregulated at 24 h post infestation than at 12 h, indicating an increased immunity induced by whitefly infestation. In contrast, genes associated with energy metabolism, carbohydrate metabolism, ribosomes, and photosynthesis are suppressed, suggesting impaired plant development. Taken together, our study provides comprehensive insights into how plants respond to phloem-feeding insects, and offers a theoretical basis for better research on plant–insect interactions. Full article
(This article belongs to the Special Issue Genetic Regulation of Biotic Stress Responses)
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18 pages, 638 KiB  
Review
Biological Embedding of Early-Life Adversity and a Scoping Review of the Evidence for Intergenerational Epigenetic Transmission of Stress and Trauma in Humans
by Aoshuang Zhou and Joanne Ryan
Genes 2023, 14(8), 1639; https://doi.org/10.3390/genes14081639 - 17 Aug 2023
Cited by 16 | Viewed by 4907
Abstract
Severe or chronic stress and trauma can have a detrimental impact on health. Evidence suggests that early-life adversity can become biologically embedded and has the potential to influence health outcomes decades later. Epigenetics is one mechanism that has been implicated in these long-lasting [...] Read more.
Severe or chronic stress and trauma can have a detrimental impact on health. Evidence suggests that early-life adversity can become biologically embedded and has the potential to influence health outcomes decades later. Epigenetics is one mechanism that has been implicated in these long-lasting effects. Observational studies in humans indicate that the effects of stress could even persist across generations, although whether or not epigenetic mechanisms are involved remains under debate. Here, we provide an overview of studies in animals and humans that demonstrate the effects of early-life stress on DNA methylation, one of the most widely studied epigenetic mechanisms, and summarize findings from animal models demonstrating the involvement of epigenetics in the transmission of stress across generations. We then describe the results of a scoping review to determine the extent to which the terms intergenerational or transgenerational have been used in human studies investigating the transmission of trauma and stress via epigenetic mechanisms. We end with a discussion of key areas for future research to advance understanding of the role of epigenetics in the legacy effects of stress and trauma. Full article
(This article belongs to the Section Epigenomics)
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29 pages, 24173 KiB  
Article
Exploring the Binding Affinity of the ARR2 GARP DNA Binding Domain via Comparative Methods
by Janine Rieger, Michael Fitz, Stefan Markus Fischer, Niklas Wallmeroth, Hector Flores-Romero, Nina Monika Fischer, Luise Helene Brand, Ana J. García-Sáez, Kenneth Wayne Berendzen and Virtudes Mira-Rodado
Genes 2023, 14(8), 1638; https://doi.org/10.3390/genes14081638 - 17 Aug 2023
Cited by 1 | Viewed by 1565
Abstract
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these [...] Read more.
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure and function of this type of DNA-binding domain; thus, how ARRs bind to DNA at a structural level is still poorly understood. In order to understand how the MSP functions in planta, it is crucial to unravel both the kinetics as well as the structural identity of the components involved in such interactions. For this reason, this work focusses on resolving how the GARP domain of ARR2 (GARP2) binds to the promoter region of ARR5, one of its native target genes in cytokinin signaling. We have established that GARP2 specifically binds to the ARR5 promoter with three different bi-molecular interaction systems—qDPI-ELISA, FCS, and MST—and we also determined the KD of this interaction. In addition, structural modeling of the GARP2 domain confirms that GARP2 entails a HTH motif, and that protein–DNA interaction most likely occurs via the α3-helix and the N-terminal arm of this domain since mutations in this region hinder ARR2’s ability to activate transcription. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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14 pages, 3508 KiB  
Article
Refinement of Leishmania donovani Genome Annotations in the Light of Ribosome-Protected mRNAs Fragments (Ribo-Seq Data)
by Alejandro Sánchez-Salvador, Sandra González-de la Fuente, Begoña Aguado, Phillip A. Yates and Jose M. Requena
Genes 2023, 14(8), 1637; https://doi.org/10.3390/genes14081637 - 17 Aug 2023
Cited by 1 | Viewed by 1574
Abstract
Advances in next-generation sequencing methodologies have facilitated the assembly of an ever-increasing number of genomes. Gene annotations are typically conducted via specialized software, but the most accurate results require additional manual curation that incorporates insights derived from functional and bioinformatic analyses (e.g., transcriptomics, [...] Read more.
Advances in next-generation sequencing methodologies have facilitated the assembly of an ever-increasing number of genomes. Gene annotations are typically conducted via specialized software, but the most accurate results require additional manual curation that incorporates insights derived from functional and bioinformatic analyses (e.g., transcriptomics, proteomics, and phylogenetics). In this study, we improved the annotation of the Leishmania donovani (strain HU3) genome using publicly available data from the deep sequencing of ribosome-protected mRNA fragments (Ribo-Seq). As a result of this analysis, we uncovered 70 previously non-annotated protein-coding genes and improved the annotation of around 600 genes. Additionally, we present evidence for small upstream open reading frames (uORFs) in a significant number of transcripts, indicating their potential role in the translational regulation of gene expression. The bioinformatics pipelines developed for these analyses can be used to improve the genome annotations of other organisms for which Ribo-Seq data are available. The improvements provided by these studies will bring us closer to the ultimate goal of a complete and accurately annotated L. donovani genome and will enhance future transcriptomics, proteomics, and genetics studies. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2023)
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6 pages, 333 KiB  
Brief Report
Steadfast Toll Like Receptor 4 (TLR4) 5-Hydroxymethylcytosine Levels in Cell-Free DNA: A Promising Consistency Marker for Colorectal Cancer Patients
by Daša Jevšinek Skok and Nina Hauptman
Genes 2023, 14(8), 1636; https://doi.org/10.3390/genes14081636 - 17 Aug 2023
Viewed by 1218
Abstract
Cell-free DNA (cfDNA) from patient blood is emerging as a noninvasive diagnostic avenue for various cancers. We aimed to identify reliable biomarkers in cfDNA by investigating genes exhibiting significant differences between colorectal cancer and control samples. Our objective was to identify genes that [...] Read more.
Cell-free DNA (cfDNA) from patient blood is emerging as a noninvasive diagnostic avenue for various cancers. We aimed to identify reliable biomarkers in cfDNA by investigating genes exhibiting significant differences between colorectal cancer and control samples. Our objective was to identify genes that showed a positive difference between cancer and control samples. To achieve this, we conducted an in silico analysis to identify genes that exhibit no significant variation in methylation between genomic DNA (gDNA) and cfDNA. We collected experimental data from publicly available repositories, which included 5-hydroxymethylcytosine (5hmC) profiles of gDNA and cfDNA samples from both cancer patients and healthy individuals. By comparing and overlapping these two groups, we identified 187 genes of interest, of which 53 genes had a positive difference among colon cancer patients and healthy individuals. Next, we performed an ANOVA test on these genes, resulting in the identification of 12 genes that showed statistically significant higher levels of 5hmC in cfDNA and gDNA from cancer patients compared to healthy individuals. Additionally, we compared the 5hmC status of these genes between cfDNA and gDNA from cancer patients. Interestingly, we found that the 5hmC of the toll like receptor 4 (TLR4) gene was not statistically different between cfDNA and gDNA from cancer patients, indicating consistency between cfDNA and gDNA. These findings have important implications, not only for experimental validation but also for the development of more sensitive and robust noninvasive methods to improve diagnostic, prognostic, and treatment options for colon cancer. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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14 pages, 10986 KiB  
Article
Spontaneous Emergence of Multicellular Heritability
by Seyed Alireza Zamani-Dahaj, Anthony Burnetti, Thomas C. Day, Peter J. Yunker, William C. Ratcliff and Matthew D. Herron
Genes 2023, 14(8), 1635; https://doi.org/10.3390/genes14081635 - 17 Aug 2023
Cited by 7 | Viewed by 1952
Abstract
The major transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long [...] Read more.
The major transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long been considered a stumbling block for nascent evolutionary transitions. Using analytical models, synthetic biology, and biologically-informed simulations, we explored the emergence of trait heritability during the evolution of multicellularity. Prior work on the evolution of multicellularity has asserted that substantial collective-level trait heritability either emerges only late in the transition or requires some evolutionary change subsequent to the formation of clonal multicellular groups. In a prior analytical model, we showed that collective-level heritability not only exists but is usually more heritable than the underlying cell-level trait upon which it is based, as soon as multicellular groups form. Here, we show that key assumptions and predictions of that model are borne out in a real engineered biological system, with important implications for the emergence of collective-level heritability. Full article
(This article belongs to the Special Issue The Genetics and Evolution of Multicellularity)
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11 pages, 1118 KiB  
Review
Advancing Epidemiology and Genetic Approaches for the Treatment of Spinal and Bulbar Muscular Atrophy: Focus on Prevalence in the Indigenous Population of Western Canada
by Harry Wilton-Clark, Ammar Al-aghbari, Jessica Yang and Toshifumi Yokota
Genes 2023, 14(8), 1634; https://doi.org/10.3390/genes14081634 - 17 Aug 2023
Cited by 3 | Viewed by 3027
Abstract
Spinal and bulbar muscular atrophy (SBMA), also known as Kennedy’s disease, is a debilitating neuromuscular disease characterized by progressive muscular weakness and neuronal degeneration, affecting 1–2 individuals per 100,000 globally. While SBMA is relatively rare, recent studies have shown a significantly higher prevalence [...] Read more.
Spinal and bulbar muscular atrophy (SBMA), also known as Kennedy’s disease, is a debilitating neuromuscular disease characterized by progressive muscular weakness and neuronal degeneration, affecting 1–2 individuals per 100,000 globally. While SBMA is relatively rare, recent studies have shown a significantly higher prevalence of the disease among the indigenous population of Western Canada compared to the general population. The disease is caused by a pathogenic expansion of polyglutamine residues in the androgen receptor protein, which acts as a key transcriptional regulator for numerous genes. SBMA has no cure, and current treatments are primarily supportive and focused on symptom management. Recently, a form of precision medicine known as antisense therapy has gained traction as a promising therapeutic option for numerous neuromuscular diseases. Antisense therapy uses small synthetic oligonucleotides to confer therapeutic benefit by acting on pathogenic mRNA molecules, serving to either degrade pathogenic mRNA transcripts or helping to modulate splicing. Recent studies have explored the suitability of antisense therapy for the treatment of SBMA, primarily focused on gene therapy and antisense-mediated mRNA knockdown approaches. Advancements in understanding the pathogenesis of SBMA and the development of targeted therapies offer hope for improved quality of life for individuals affected by this debilitating condition. Continued research is essential to optimize these genetic approaches, ensuring their safety and efficacy. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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8 pages, 1700 KiB  
Case Report
Liver Involvement in Patients with Rare MBOAT7 Variants and Intellectual Disability: A Case Report and Literature Review
by Luisa Ronzoni, Matteo Mureddu, Francesco Malvestiti, Vittoria Moretti, Cristiana Bianco, Giulia Periti, Margherita Baldassarri, Francesca Ariani, Anna Carrer, Serena Pelusi, Alessandra Renieri, Daniele Prati and Luca Valenti
Genes 2023, 14(8), 1633; https://doi.org/10.3390/genes14081633 - 16 Aug 2023
Cited by 2 | Viewed by 1679
Abstract
The membrane-bound O-acyltransferase domain-containing 7 (MBOAT7) protein is an acyltransferase catalyzing arachidonic acid incorporation into lysophosphatidylinositol. Patients with rare, biallelic loss-of-function variants of the MBOAT7 gene display intellectual disability with neurodevelopmental defects. The rs641738 inherited variant associated with reduced hepatic MBOAT7 expression has [...] Read more.
The membrane-bound O-acyltransferase domain-containing 7 (MBOAT7) protein is an acyltransferase catalyzing arachidonic acid incorporation into lysophosphatidylinositol. Patients with rare, biallelic loss-of-function variants of the MBOAT7 gene display intellectual disability with neurodevelopmental defects. The rs641738 inherited variant associated with reduced hepatic MBOAT7 expression has been linked to steatotic liver disease susceptibility. However, the impact of biallelic loss-of-function MBOAT7 variants on liver disease is not known. We report on a 2-year-old girl with MBOAT7-related intellectual disability and steatotic liver disease, confirming that MBOAT7 loss-of-function predisposes to liver disease. Full article
(This article belongs to the Collection Genetics and Genomics of Rare Disorders)
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7 pages, 875 KiB  
Case Report
A Rare Pathological Phenotype of Endometrioid Serous and Clear-Cell Ovarian Cancer with PIK3CA Mutations in Relation to The Excellent Response of Alpelisib
by Ertugrul Bayram, Ghanim Khatib, Burak Guney, Emine Kilicbagir, Huru Rabia Gulec, Ibrahim Boga and Semra Paydas
Genes 2023, 14(8), 1632; https://doi.org/10.3390/genes14081632 - 16 Aug 2023
Viewed by 1589
Abstract
Patients with metastatic ovarian cancer who develop resistance to standard therapy with or without platinum need to search for other therapeutic choices. Therefore, identifying genetic alterations and selecting an approach to treatment using precision medicine techniques are important. In a patient diagnosed with [...] Read more.
Patients with metastatic ovarian cancer who develop resistance to standard therapy with or without platinum need to search for other therapeutic choices. Therefore, identifying genetic alterations and selecting an approach to treatment using precision medicine techniques are important. In a patient diagnosed with mixed-type ovarian cancer after surgery, adjuvant therapy was applied with a combination of carboplatin and taxane, but the disease recurred. Upon evaluation of the patient as having platinum-sensitive epithelial ovarian cancer (EOC), combination therapy with bevacizumab was initially successful. However, disease progression was again observed, and molecular analysis revealed the presence of an E545K mutation in the PIK3CA gene; therefore, a selective PI3K inhibitor, alpelisib, was used as a treatment under the compassionate-use protocol. The patient’s complications improved after receiving the alpelisib medication. The patient has been in complete remission for over two years. This case serves as a rare example that confirms the utility of alpelisib in managing mixed-type ovarian cancer. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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