Genes

12 pages, 287 KiB

Open AccessReview

National Genome Initiatives in Europe and the United Kingdom in the Era of Whole-Genome Sequencing: A Comprehensive Review

by Jan Smetana and Petr Brož

Genes 2022, 13(3), 556; https://doi.org/10.3390/genes13030556 - 21 Mar 2022

Cited by 11 | Viewed by 4336

Abstract

Identification of genomic variability in population plays an important role in the clinical diagnostics of human genetic diseases. Thanks to rapid technological development in the field of massive parallel sequencing technologies, also known as next-generation sequencing (NGS), complex genomic analyses are now easier [...] Read more.

Identification of genomic variability in population plays an important role in the clinical diagnostics of human genetic diseases. Thanks to rapid technological development in the field of massive parallel sequencing technologies, also known as next-generation sequencing (NGS), complex genomic analyses are now easier and cheaper than ever before, which consequently leads to more effective utilization of these techniques in clinical practice. However, interpretation of data from NGS is still challenging due to several issues caused by natural variability of DNA sequences in human populations. Therefore, development and realization of projects focused on description of genetic variability of local population (often called “national or digital genome”) with a NGS technique is one of the best approaches to address this problem. The next step of the process is to share such data via publicly available databases. Such databases are important for the interpretation of variants with unknown significance or (likely) pathogenic variants in rare diseases or cancer or generally for identification of pathological variants in a patient’s genome. In this paper, we have compiled an overview of published results of local genome sequencing projects from United Kingdom and Europe together with future plans and perspectives for newly announced ones. Full article

(This article belongs to the Special Issue Revealing the Genomic Big Data: How Much Information Is Ready for Clinical Application?)

15 pages, 4178 KiB

Open AccessArticle

Expression Analysis of the TdDRF1 Gene in Field-Grown Durum Wheat under Full and Reduced Irrigation

by Arianna Latini, Cristina Cantale, Karthikeyan Thiyagarajan, Karim Ammar and Patrizia Galeffi

Genes 2022, 13(3), 555; https://doi.org/10.3390/genes13030555 - 21 Mar 2022

Cited by 2 | Viewed by 2809

Abstract

Some of the key genes and regulatory mechanisms controlling drought response in durum wheat have been identified. One of the major challenges for breeders is how to use this knowledge for the achievement of drought stress tolerance. In the present study, we report [...] Read more.

Some of the key genes and regulatory mechanisms controlling drought response in durum wheat have been identified. One of the major challenges for breeders is how to use this knowledge for the achievement of drought stress tolerance. In the present study, we report the expression profiles of the TdDRF1 gene, at consecutive plant growth stages, from different durum wheat genotypes evaluated in two different field environments. The expression of a possible target gene (Wdnh13) of the TdDRF1 gene was also investigated and analogies with the transcript profiles were found. The results of the qRT-PCR highlighted differences in molecular patterns, thus suggesting a genotype dependency of the TdDRF1 gene expression in response to the stress induced. Furthermore, a statistical association between the expression of TdDRF1 transcripts and agronomic traits was also performed and significant differences were found among genotypes, suggesting a relationship. One of the genotypes was found to combine molecular and agronomic characteristics. Full article

(This article belongs to the Special Issue Genetics and Evolution of Abiotic Stress Tolerance in Plants)

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15 pages, 688 KiB

Open AccessArticle

Note on DNA Analysis and Redesigning Using Markov Chain

by Maciej Zakarczemny and Małgorzata Zajęcka

Genes 2022, 13(3), 554; https://doi.org/10.3390/genes13030554 - 21 Mar 2022

Cited by 2 | Viewed by 2237

Abstract

The paper contains a discussion on mathematical modifying and redesigning DNA with the use of Markov chains. We give a simple mathematical technique for overwriting missing parts of DNA. With a certain probability (without even knowing the function of the missing codon) we [...] Read more.

The paper contains a discussion on mathematical modifying and redesigning DNA with the use of Markov chains. We give a simple mathematical technique for overwriting missing parts of DNA. With a certain probability (without even knowing the function of the missing codon) we can find a synonymous codon, so that there is no frequency change in amino acid sequences of proteins. We use Markov Chain to analyze the dependencies in DNA sequence of the human gene Alpha 1,3-Galactosyltransfe rase 2. We include a theoretical introduction which facilitates the understanding of the paper for non-mathematicians, especially for biologists not familiar with the theory of Markov chains. Full article

(This article belongs to the Section Bioinformatics)

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16 pages, 1850 KiB

Open AccessArticle

Gnas Promoter Hypermethylation in the Basolateral Amygdala Regulates Reconsolidation of Morphine Reward Memory in Rats

by Peng Liu, Jialong Liang, Fengze Jiang, Wanshi Cai, Fang Shen, Jing Liang, Jianjun Zhang, Zhongsheng Sun and Nan Sui

Genes 2022, 13(3), 553; https://doi.org/10.3390/genes13030553 - 21 Mar 2022

Cited by 6 | Viewed by 2851

Abstract

Impairing reconsolidation may disrupt drug memories to prevent relapse, meanwhile long-term transcription regulations in the brain regions contribute to the occurrence of emotional memories. The basolateral amygdala (BLA) is involved in the drug-cue association, while the nucleus accumbens (NAc) responds to the drug [...] Read more.

Impairing reconsolidation may disrupt drug memories to prevent relapse, meanwhile long-term transcription regulations in the brain regions contribute to the occurrence of emotional memories. The basolateral amygdala (BLA) is involved in the drug-cue association, while the nucleus accumbens (NAc) responds to the drug reward. Here, we assessed whether DNA methyltransferases (Dnmts) in these two brain regions function identically in the reconsolidation of morphine reward memory. We show that Dnmts inhibition in the BLA but not in the NAc after memory retrieval impaired reconsolidation of a morphine reward memory. Moreover, the mRNA levels of Dnmt3a and Dnmt3b, rather than Dnmt1, in the BLA were continuously upregulated after retrieval. We further identified the differentially methylated regions (DMRs) in genes in the BLA after retrieval, and focused on the DMRs located in gene promoter regions. Among them were three genes (Gnas, Sox10, and Pik3r1) involved in memory modulation. Furthermore, Gnas promoter hypermethylation was confirmed to be inversely correlated with the downregulation of Gnas mRNA levels. The findings indicate that the specific transcription regulation mechanism in the BLA and NAc on reconsolidation of opiate-associated memories can be dissociable, and DNA hypermethylation of Gnas in the BLA is necessary for the reconsolidation of morphine reward memories. Full article

(This article belongs to the Special Issue Genetics and Genomics of Addiction)

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15 pages, 2956 KiB

Open AccessArticle

Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic

by Muhammad Zeeshan Anwar, Madeeha Shahzad Lodhi, Muhammad Tahir Khan, Malik Ihsanullah Khan and Sumaira Sharif

Genes 2022, 13(3), 552; https://doi.org/10.3390/genes13030552 - 21 Mar 2022

Cited by 15 | Viewed by 3589

Abstract

Genomic epidemiology of SARS-CoV-2 is imperative to explore the transmission, evolution, and also pathogenicity of viruses. The emergence of SARS-CoV-2 variants of concern posed a severe threat to the global public health efforts. To assess the potential consequence of these emerging variants on [...] Read more.

Genomic epidemiology of SARS-CoV-2 is imperative to explore the transmission, evolution, and also pathogenicity of viruses. The emergence of SARS-CoV-2 variants of concern posed a severe threat to the global public health efforts. To assess the potential consequence of these emerging variants on public health, continuous molecular epidemiology is of vital importance. The current study has been designed to investigate the major SARS-CoV-2 variants and emerging mutations in virus structural and non-structural proteins (NSP) during the fourth wave in September 2021 from the Punjab province of Pakistan. Twenty SARS-CoV-2 positive samples have been collected from major cities were subjected to next-generation sequencing. Among the 20 whole genomes (GenBank Accession SRR16294858-SRR16294877), 2 samples failed to be completely sequenced. These genome sequences harbored 207 non-synonymous mutations, among which 19 were unique to GISAID. The genome sequences were detected: Delta 21I, 21J variants (B.1.617.2). Mutation’s spike_F157del, spike_P681R, spike_T478K, spike_T19R, spike_L452R, spike_D614G, spike_G142D, spike_E156G, and spike_R158del have been detected in all samples where K1086Q, E554K, and C1250W were unique in spike protein. These genomic sequences also harbored 129 non-synonymous mutations in NSP. The most common were NSP3_P1469S (N = 17), NSP3_A488S (N = 17), NSP3_P1228L (N = 17), NSP4_V167L (N = 17), NSP4_T492I (N = 17), NSP6_T77A (N = 17), NSP14_A394V (N = 17), NSP12_G671S (N = 18), and NSP13_P77L (N = 18). The mutation, F313Y in NSP12, detected in the current study, was found in a single isolate from Belgium. Numerous other unique mutations have been detected in the virus papain-like protease (NSP3), main protease (NSP5), and RNA-dependent RNA polymerase (NSP12). The most common non-synonymous mutations in the spike protein were subjected to stability analysis, exhibiting a stabilizing effect on structures. The presence of Delta variants may affect therapeutic efforts and vaccine efficacy. Continuous genomic epidemiology of SARS-CoV-2 in Pakistan may be useful for better management of SARS-CoV-2 infections. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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26 pages, 4875 KiB

Open AccessArticle

In Vitro Analysis of Biological Activity of Circulating Cell-Free DNA Isolated from Blood Plasma of Schizophrenic Patients and Healthy Controls

by Elizaveta S. Ershova, Galina V. Shmarina, Lev N. Porokhovnik, Natalia V. Zakharova, George P. Kostyuk, Pavel E. Umriukhin, Sergey I. Kutsev, Vasilina A. Sergeeva, Natalia N. Veiko and Svetlana V. Kostyuk

Genes 2022, 13(3), 551; https://doi.org/10.3390/genes13030551 - 20 Mar 2022

Cited by 8 | Viewed by 3711

Abstract

Schizophrenia is associated with low-grade systemic inflammation. Circulating cell-free DNA (c-cfDNA) belongs to the DAMP class. The major research question was: can the c-cfDNA of schizophrenic patients (sz-cfDNA) stimulate the DNA sensor genes, which control the innate immunity? We investigated the in vitro [...] Read more.

Schizophrenia is associated with low-grade systemic inflammation. Circulating cell-free DNA (c-cfDNA) belongs to the DAMP class. The major research question was: can the c-cfDNA of schizophrenic patients (sz-cfDNA) stimulate the DNA sensor genes, which control the innate immunity? We investigated the in vitro response of ten human skin fibroblast (HSF) lines to five DNA probes containing different amounts of a GC-rich marker (the ribosomal repeat) and a DNA oxidation marker (8-oxodG) including sz-cfDNA and healthy control c-cfDNA (hc-cfDNA) probes. After 1 h, 3 h, and 24 h of incubation, the expression of 6 protein genes responsible for cfDNA transport into the cell (EEA1 and HMGB1) and the recognition of cytosolic DNA (TLR9, AIM2, STING and RIG-I) was analyzed at the transcriptional (RT-qPCR) and protein level (flow cytometry and fluorescence microscopy). Additionally, we analyzed changes in the RNA amount of 32 genes (RT-qPCR), which had been previously associated with different cellular responses to cell-free DNA with different characteristics. Adding sz-cfDNA and hc-cfDNA to the HSF medium in equal amounts (50 ng/mL) blocked endocytosis and stimulated TLR9 and STING gene expression while blocking RIG-I and AIM2 expression. Sz-cfDNA and hc-cfDNA, compared to gDNA, demonstrated much stronger stimulated transcription of genes that control cell proliferation, cytokine synthesis, apoptosis, autophagy, and mitochondrial biogenesis. No significant difference was observed in the response of the cells to sz-cfDNA and hc-cfDNA. Sz-cfDNA and hc-cfDNA showed similarly high biological activity towards HSFs, stimulating the gene activity of TLR9 and STING DNA sensor proteins and blocking the activity of the AIM2 protein gene. Since the sz-cfDNA content in the patients’ blood is several times higher than the hc-cfDNA content, sz-cfDNA may upregulate pro-inflammatory cytokines in schizophrenia. Full article

(This article belongs to the Special Issue Genomics of Neuropsychiatric Disorders)

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14 pages, 2263 KiB

Open AccessReview

Rif1-Dependent Control of Replication Timing

by Logan Richards, Souradip Das and Jared T. Nordman

Genes 2022, 13(3), 550; https://doi.org/10.3390/genes13030550 - 20 Mar 2022

Cited by 16 | Viewed by 4093

Abstract

Successful duplication of the genome requires the accurate replication of billions of base pairs of DNA within a relatively short time frame. Failure to accurately replicate the genome results in genomic instability and a host of diseases. To faithfully and rapidly replicate the [...] Read more.

Successful duplication of the genome requires the accurate replication of billions of base pairs of DNA within a relatively short time frame. Failure to accurately replicate the genome results in genomic instability and a host of diseases. To faithfully and rapidly replicate the genome, DNA replication must be tightly regulated and coordinated with many other nuclear processes. These regulations, however, must also be flexible as replication kinetics can change through development and differentiation. Exactly how DNA replication is regulated and how this regulation changes through development is an active field of research. One aspect of genome duplication where much remains to be discovered is replication timing (RT), which dictates when each segment of the genome is replicated during S phase. All organisms display some level of RT, yet the precise mechanisms that govern RT remain are not fully understood. The study of Rif1, a protein that actively regulates RT from yeast to humans, provides a key to unlock the underlying molecular mechanisms controlling RT. The paradigm for Rif1 function is to delay helicase activation within certain regions of the genome, causing these regions to replicate late in S phase. Many questions, however, remain about the intricacies of Rif1 function. Here, we review the current models for the activity of Rif1 with the goal of trying to understand how Rif1 functions to establish the RT program. Full article

(This article belongs to the Special Issue DNA Replication Kinetics)

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14 pages, 3171 KiB

Open AccessArticle

Expression of HK2, PKM2, and PFKM Is Associated with Metastasis and Late Disease Onset in Breast Cancer Patients

by Mehreen Ishfaq, Nabiha Bashir, Syeda Kiran Riaz, Shumaila Manzoor, Jahangir Sarwar Khan, Yamin Bibi, Rokayya Sami, Amani H. Aljahani, Saif A. Alharthy and Ramla Shahid

Genes 2022, 13(3), 549; https://doi.org/10.3390/genes13030549 - 20 Mar 2022

Cited by 15 | Viewed by 3697

Abstract

The reprogramming of energy metabolism is one of the hallmarks of cancer and is crucial for tumor progression. Altered aerobic glycolysis is a well-known characteristic of cancer cell metabolism. In the present study, the expression profiles of key metabolic genes (HK2, [...] Read more.

The reprogramming of energy metabolism is one of the hallmarks of cancer and is crucial for tumor progression. Altered aerobic glycolysis is a well-known characteristic of cancer cell metabolism. In the present study, the expression profiles of key metabolic genes (HK2, PFKM, and PKM2) were assessed in the breast cancer cohort of Pakistan using quantitative polymerase chain reaction (qPCR) and IHC. Expression patterns were correlated with molecular subtypes and clinical parameters in the patients. A significant upregulation of key glycolytic genes was observed in tumor samples in comparison to their adjacent controls (p < 0.0001). The expression of the studied glycolytic genes was significantly increased in late clinical stages, positive nodal involvement, and distant metastasis (p < 0.05). HK2 and PKM2 were found to be upregulated in luminal B, whereas PFKM was overexpressed in the luminal A subtype of breast cancer. The genes were positively correlated with the proliferation marker Ki67 (p < 0.001). Moreover, moderate positive linear correlations between HK2 and PKM2 (r = 0.476), HK2 and PFKM (r = 0.473), and PKM2 and PFKM (r = 0.501) were also observed (p < 0.01). These findings validate that the key regulatory genes in glycolysis can serve as potential biomarkers and/or molecular targets for breast cancer management. However, the clinical significance of these molecules needs to be further validated through in vitro and in vivo experiments. Full article

(This article belongs to the Special Issue Public Health Genetics and Genomics)

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10 pages, 1448 KiB

Open AccessEditor’s ChoiceArticle

Development of an HRMA-Based Marker Assisted Selection (MAS) Approach for Cost-Effective Genotyping of S and M Loci Controlling Self-Compatibility in Apricot (Prunus armeniaca L.)

by Bianca Maria Orlando Marchesano, Remo Chiozzotto, Irina Baccichet, Daniele Bassi and Marco Cirilli

Genes 2022, 13(3), 548; https://doi.org/10.3390/genes13030548 - 20 Mar 2022

Cited by 4 | Viewed by 2299

Abstract

The apricot species is characterized by a gametophytic self-incompatibility (GSI) system. While GSI is one of the most efficient mechanisms to prevent self-fertilization and increase genetic variability, it represents a limiting factor for fruit production in the orchards. Compatibility among apricot cultivars was [...] Read more.

The apricot species is characterized by a gametophytic self-incompatibility (GSI) system. While GSI is one of the most efficient mechanisms to prevent self-fertilization and increase genetic variability, it represents a limiting factor for fruit production in the orchards. Compatibility among apricot cultivars was usually assessed by either field pollination experiments or by histochemical evaluation of in vitro pollen tube growth. In apricots, self-compatibility is controlled by two unlinked loci, S and M, and associated to transposable element insertion within the coding sequence of SFB and ParM-7 genes, respectively. Self-compatibility has become a primary breeding goal in apricot breeding programmes, stimulating the development of a rapid and cost-effective marker assisted selection (MAS) approach to accelerate screening of self-compatible genotypes. In this work, we demonstrated the feasibility of a novel High Resolution Melting Analysis (HRMA) approach for the massive screening of self-compatible and self-incompatible genotypes for both S and M loci. The different genotypes were unambiguously recognized by HRMA, showing clearly distinguishable melting profiles. The assay was developed and tested in a panel of accessions and breeding selections with known self-compatibility reaction, demonstrating the potential usefulness of this approach to optimize and accelerate apricot breeding programmes. Full article

(This article belongs to the Special Issue Genetics and Genomics of Edible Rosaceae)

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20 pages, 4664 KiB

Open AccessArticle

Tissue-Specific Expression of the Terpene Synthase Family Genes in Rosa chinensis and Effect of Abiotic Stress Conditions

by Yuhang Yan, Mouliang Li, Xiaoni Zhang, Weilong Kong, Mohammed Bendahmane, Manzhu Bao and Xiaopeng Fu

Genes 2022, 13(3), 547; https://doi.org/10.3390/genes13030547 - 20 Mar 2022

Cited by 14 | Viewed by 3881

Abstract

Rose (Rosa chinensis) is one of the most famous ornamental plants worldwide, with a variety of colors and fragrances. Terpene synthases (TPSs) play critical roles in the biosynthesis of terpenes. In this work, we report a comprehensive study on the genome-wide [...] Read more.

Rose (Rosa chinensis) is one of the most famous ornamental plants worldwide, with a variety of colors and fragrances. Terpene synthases (TPSs) play critical roles in the biosynthesis of terpenes. In this work, we report a comprehensive study on the genome-wide identification and characterization of the TPS family in R. chinensis. We identified 49 TPS genes in the R. chinensis genome, and they were grouped into five subfamilies (TPS-a, TPS-b, TPS-c, TPS-g and TPS-e/f). Phylogenetics, gene structure and conserved motif analyses indicated that the RcTPS genes possessed relatively conserved gene structures and the RcTPS proteins contained relatively conserved motifs. Multiple putative cis-acting elements involved in the stress response were identified in the promoter region of RcTPS genes, suggesting that some could be regulated by stress. The expression profile of RcTPS genes showed that they were predominantly expressed in the petals of open flowers, pistils, leaves and roots. Under osmotic and heat stresses, the expression of most RcTPS genes was upregulated. These data provide a useful foundation for deciphering the functional roles of RcTPS genes during plant growth as well as addressing the link between terpene biosynthesis and abiotic stress responses in roses. Full article

(This article belongs to the Special Issue Genomic and Genetic Resources and Rose Biology and Breeding)

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9 pages, 637 KiB

Open AccessReview

Loss, Gain, and Retention: Mechanisms Driving Late Prophase I Chromosome Remodeling for Accurate Meiotic Chromosome Segregation

by Laura I. Láscarez-Lagunas, Marina Martinez-Garcia and Monica P. Colaiácovo

Genes 2022, 13(3), 546; https://doi.org/10.3390/genes13030546 - 19 Mar 2022

Cited by 3 | Viewed by 3145

Abstract

To generate gametes, sexually reproducing organisms need to achieve a reduction in ploidy, via meiosis. Several mechanisms are set in place to ensure proper reductional chromosome segregation at the first meiotic division (MI), including chromosome remodeling during late prophase I. Chromosome remodeling after [...] Read more.

To generate gametes, sexually reproducing organisms need to achieve a reduction in ploidy, via meiosis. Several mechanisms are set in place to ensure proper reductional chromosome segregation at the first meiotic division (MI), including chromosome remodeling during late prophase I. Chromosome remodeling after crossover formation involves changes in chromosome condensation and restructuring, resulting in a compact bivalent, with sister kinetochores oriented to opposite poles, whose structure is crucial for localized loss of cohesion and accurate chromosome segregation. Here, we review the general processes involved in late prophase I chromosome remodeling, their regulation, and the strategies devised by different organisms to produce bivalents with configurations that promote accurate segregation. Full article

(This article belongs to the Special Issue Genetics of Meiotic Chromosome Dynamics)

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9 pages, 427 KiB

Open AccessReview

Preferentially Expressed Antigen in Melanoma (PRAME) and Human Malignant Melanoma: A Retrospective Study

by Gerardo Cazzato, Katia Mangialardi, Giovanni Falcicchio, Anna Colagrande, Giuseppe Ingravallo, Francesca Arezzo, Giovanna Giliberti, Irma Trilli, Vera Loizzi, Teresa Lettini, Sara Scarcella, Tiziana Annese, Paola Parente, Carmelo Lupo, Nadia Casatta, Eugenio Maiorano, Gennaro Cormio, Leonardo Resta and Domenico Ribatti

Genes 2022, 13(3), 545; https://doi.org/10.3390/genes13030545 - 19 Mar 2022

Cited by 15 | Viewed by 4914

Abstract

Background: Preferentially expressed antigen in melanoma (PRAME) is a cancer testis antigen (CTA) identified in 1997 through analysis of the specificity of tumor-reactive T-cell clones derived from a patient with metastatic cutaneous melanoma. Although at first it seemed even more specific, various studies [...] Read more.

Background: Preferentially expressed antigen in melanoma (PRAME) is a cancer testis antigen (CTA) identified in 1997 through analysis of the specificity of tumor-reactive T-cell clones derived from a patient with metastatic cutaneous melanoma. Although at first it seemed even more specific, various studies have shown that PRAME can also be expressed in the context of atypical lesions that do not correspond solely to the definition of malignant melanoma. Methods: A systematic review of English articles was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results: 126 records were identified in the literature search, of which 9 were duplicates. After screening for eligibility and inclusion criteria, 53 publications were included. Conclusions: The advent of a new marker such as PRAME is surely a step forward not only in the diagnostic approach, but also in the immunotherapeutic approach to MM. However, various studies have shown that PRAME can also be expressed in the context of atypical lesions apart from MM and, for this reason, the diagnostic sensitivity and specificity (hence accuracy) are clearly lower. Further studies with larger case series will be necessary to understand better what possibilities are offered in terms of diagnostic reliability by PRAME. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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15 pages, 356 KiB

Open AccessFeature PaperArticle

Interep: An R Package for High-Dimensional Interaction Analysis of the Repeated Measurement Data

by Fei Zhou, Jie Ren, Yuwen Liu, Xiaoxi Li, Weiqun Wang and Cen Wu

Genes 2022, 13(3), 544; https://doi.org/10.3390/genes13030544 - 19 Mar 2022

Cited by 2 | Viewed by 3281

Abstract

We introduce interep, an R package for interaction analysis of repeated measurement data with high-dimensional main and interaction effects. In G × E interaction studies, the forms of environmental factors play a critical role in determining how structured sparsity should be imposed [...] Read more.

We introduce interep, an R package for interaction analysis of repeated measurement data with high-dimensional main and interaction effects. In G × E interaction studies, the forms of environmental factors play a critical role in determining how structured sparsity should be imposed in the high-dimensional scenario to identify important effects. Zhou et al. (2019) (PMID: 31816972) proposed a longitudinal penalization method to select main and interaction effects corresponding to the individual and group structure, respectively, which requires a mixture of individual and group level penalties. The R package interep implements generalized estimating equation (GEE)-based penalization methods with this sparsity assumption. Moreover, alternative methods have also been implemented in the package. These alternative methods merely select effects on an individual level and ignore the group-level interaction structure. In this software article, we first introduce the statistical methodology corresponding to the penalized GEE methods implemented in the package. Next, we present the usage of the core and supporting functions, which is followed by a simulation example with R codes and annotations. The R package interep is available at The Comprehensive R Archive Network (CRAN). Full article

(This article belongs to the Special Issue Statistical Genetics in Human Diseases)

9 pages, 1547 KiB

Open AccessBrief Report

Identification of Frameshift Variants in POLH Gene Causing Xeroderma Pigmentosum in Two Consanguineous Pakistani Families

by Ghazala Y. Zamani, Ranjha Khan, Noreen Karim, Zubair M. Ahmed and Muhammad Naeem

Genes 2022, 13(3), 543; https://doi.org/10.3390/genes13030543 - 19 Mar 2022

Viewed by 2868

Abstract

Xeroderma pigmentosum (XP) is a rare autosomal recessive genetic disorder characterized by severe sensitivity of skin to sunlight and an increased risk of skin cancer. XP variant (XPV), a milder subtype, is caused by variants in the POLH gene. POLH encodes an error-prone [...] Read more.

Xeroderma pigmentosum (XP) is a rare autosomal recessive genetic disorder characterized by severe sensitivity of skin to sunlight and an increased risk of skin cancer. XP variant (XPV), a milder subtype, is caused by variants in the POLH gene. POLH encodes an error-prone DNA-polymerase eta (pol eta) which performs translesion synthesis past ultraviolet photoproducts. The current study documents the clinical and genetic investigations of two large consanguineous Pakistani families affected with XPV. In family 1, whole exome sequencing (WES) revealed a novel frameshift variant, c.1723dupG (p.(Val575Glyfs*4)), of POLH, which is predicted to cause frameshift and premature truncation of the encoded enzyme. Indeed, our ex vivo studies in HEK293T cells confirmed the truncation of the encoded protein due to the c.1723dupG variant. In family 2, Sanger sequencing of POLH exons, revealed a recurrent nonsense variant, c.437dupA (p.Tyr146*). POLH forms a hetero-tetrameric POLZ complex with REV3L, REV7, POLD2 and POLD3. Next, we performed in silico analysis of POLH and other POLZ complex genes expression in publicly available single cell mRNAseq datasets from adult human healthy and aging skin. We found overlapping expression of POLH, REV3L and POLD2 in multiple cell types including differentiated and undifferentiated keratinocytes, pericytes and melanocytes in healthy skin. However, in aging human skin, POLH expression is reduced in compare to its POLZ complex partners. Insights from our study will facilitate counseling regarding the molecular and phenotypic landscape of POLH-related XPV. Full article

(This article belongs to the Special Issue Molecular Basis of Rare Diseases)

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19 pages, 3672 KiB

Open AccessArticle

Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Alliumcepa L.)

by Hyun-Min Lee, Jee-Soo Park, So-Jeong Kim, Seung-Gyu Kim and Young-Doo Park

Genes 2022, 13(3), 542; https://doi.org/10.3390/genes13030542 - 18 Mar 2022

Cited by 7 | Viewed by 2895

Abstract

Gray mold disease caused by Botrytis in onions (Allium cepa L.) during growth and storage negatively affects their yield and quality. Exploring the genes related to gray mold resistance in onion and their application to the breeding of resistant onion lines will [...] Read more.

Gray mold disease caused by Botrytis in onions (Allium cepa L.) during growth and storage negatively affects their yield and quality. Exploring the genes related to gray mold resistance in onion and their application to the breeding of resistant onion lines will support effective and ecological control methods of the disease. Here, the genetic relationship of 54 onion lines based on random amplified polymorphic DNA (RAPD) and in vitro-cultured onion lines infected with gray mold were used for screening resistance and susceptibility traits. Two genetically related onion lines were selected, one with a resistant and one with a susceptible phenotype. In vitro gray mold infection was repeated with these two lines, and leaf samples were collected for gene expression studies in time series. Transcript sequences obtained by RNA sequencing were subjected to DEG analysis, variant analysis, and KEGG mapping. Among the KEGG pathways, ‘α-linoleic acid metabolism’ was selected because the comparison of the time series expression pattern of Jasmonate resistant 1 (JAR1), Coronatine-insensitive protein 1 (COI 1), and transcription factor MYC2 (MYC2) genes between the resistant and susceptible lines revealed its significant relationship with gray-mold-resistant phenotypes. Expression pattern and SNP of the selected genes were verified by quantitative real-time PCR and high-resolution melting (HRM) analysis, respectively. The results of this study will be useful for the development of molecular marker and finally breeding of gray-mold-resistant onions. Full article

(This article belongs to the Special Issue Genetic Research and Plant Breeding)

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12 pages, 1396 KiB

Open AccessArticle

Demographic Reconstruction of Antarctic Fur Seals Supports the Krill Surplus Hypothesis

by Joseph I. Hoffman, Rebecca S. Chen, David L. J. Vendrami, Anna J. Paijmans, Kanchon K. Dasmahapatra and Jaume Forcada

Genes 2022, 13(3), 541; https://doi.org/10.3390/genes13030541 - 18 Mar 2022

Cited by 14 | Viewed by 4532

Abstract

Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may [...] Read more.

Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the ‘krill surplus hypothesis’. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology. Full article

(This article belongs to the Special Issue Polar Genomics)

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25 pages, 1714 KiB

Open AccessReview

Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches

by Rebecca J. D’Esposito, Christopher A. Myers, Alan A. Chen and Sweta Vangaveti

Genes 2022, 13(3), 540; https://doi.org/10.3390/genes13030540 - 18 Mar 2022

Cited by 8 | Viewed by 4241

Abstract

RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many [...] Read more.

RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration. Full article

(This article belongs to the Special Issue RNA Chemical Biology)

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17 pages, 1683 KiB

Open AccessArticle

Telomeric Repeat-Containing RNA (TERRA): A Review of the Literature and First Assessment in Cutaneous T-Cell Lymphomas

by Alain Chebly, Joana Ropio, Lyla Baldasseroni, Martina Prochazkova-Carlotti, Yamina Idrissi, Jacky Ferrer, Chantal Farra, Marie Beylot-Barry, Jean-Philippe Merlio and Edith Chevret

Genes 2022, 13(3), 539; https://doi.org/10.3390/genes13030539 - 18 Mar 2022

Cited by 9 | Viewed by 4670

Abstract

Telomeric Repeat-containing RNA (TERRA) are long non-coding RNAs transcribed from telomeric DNA sequences from multiple chromosome ends. Major research efforts have been made to understand TERRA roles and functions in several physiological and pathological processes. We summarize herein available data regarding TERRA’s roles [...] Read more.

Telomeric Repeat-containing RNA (TERRA) are long non-coding RNAs transcribed from telomeric DNA sequences from multiple chromosome ends. Major research efforts have been made to understand TERRA roles and functions in several physiological and pathological processes. We summarize herein available data regarding TERRA’s roles in human cells and we report the first investigation in cutaneous T-cells lymphomas (CTCL) using real-time PCR. Among the TERRA analysed, our data suggest a particular role for TERRA 16p downregulation and TERRA 11q upregulation in CTCL lymphomagenesis. Full article

(This article belongs to the Section Epigenomics)

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16 pages, 1480 KiB

Open AccessArticle

Transcriptomics of Wet Skin Biopsies Predict Early Radiation-Induced Hematological Damage in a Mouse Model

by Abdulnaser Alkhalil, John Clifford, Stacy Ann Miller, Aarti Gautam, Marti Jett, Rasha Hammamieh, Lauren T. Moffatt and Jeffrey W. Shupp

Genes 2022, 13(3), 538; https://doi.org/10.3390/genes13030538 - 18 Mar 2022

Viewed by 2485

Abstract

The lack of an easy and fast radiation-exposure testing method with a dosimetric ability complicates triage and treatment in response to a nuclear detonation, radioactive material release, or clandestine exposure. The potential of transcriptomics in radiation diagnosis and prognosis were assessed here using [...] Read more.

The lack of an easy and fast radiation-exposure testing method with a dosimetric ability complicates triage and treatment in response to a nuclear detonation, radioactive material release, or clandestine exposure. The potential of transcriptomics in radiation diagnosis and prognosis were assessed here using wet skin (blood/skin) biopsies obtained at hour 2 and days 4, 7, 21, and 28 from a mouse radiation model. Analysis of significantly differentially transcribed genes (SDTG; p ≤ 0.05 and FC ≥ 2) during the first post-exposure week identified the glycoprotein 6 (GP-VI) signaling, the dendritic cell maturation, and the intrinsic prothrombin activation pathways as the top modulated pathways with stable inactivation after lethal exposures (20 Gy) and intermittent activation after sublethal (1, 3, 6 Gy) exposure time points (TPs). Interestingly, these pathways were inactivated in the late TPs after sublethal exposure in concordance with a delayed deleterious effect. Modulated transcription of a variety of collagen types, laminin, and peptidase genes underlay the modulated functions of these hematologically important pathways. Several other SDTGs related to platelet and leukocyte development and functions were identified. These results outlined genetic determinants that were crucial to clinically documented radiation-induced hematological and skin damage with potential countermeasure applications. Full article

(This article belongs to the Collection Feature Papers in ‘Animal Genetics and Genomics’)

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28 pages, 1508 KiB

Open AccessArticle

SOD-1 Variants in Amyotrophic Lateral Sclerosis: Systematic Re-Evaluation According to ACMG-AMP Guidelines

by Paola Ruffo, Benedetta Perrone and Francesca Luisa Conforti

Genes 2022, 13(3), 537; https://doi.org/10.3390/genes13030537 - 18 Mar 2022

Cited by 11 | Viewed by 4565

Abstract

Amyotrophic lateral sclerosis (ALS) is the most common type of motor neuron disease whose causes are unclear. The first ALS gene associated with the autosomal dominant form of the disease was SOD1. This gene has a high rate of rare variants, and [...] Read more.

Amyotrophic lateral sclerosis (ALS) is the most common type of motor neuron disease whose causes are unclear. The first ALS gene associated with the autosomal dominant form of the disease was SOD1. This gene has a high rate of rare variants, and an appropriate classification is essential for a correct ALS diagnosis. In this study, we re-evaluated the classification of all previously reported SOD1 variants (n = 202) from ALSoD, project MinE, and in-house databases by applying the ACMG-AMP criteria to ALS. New bioinformatics analysis, frequency rating, and a thorough search for functional studies were performed. We also proposed adjusting criteria strength describing how to apply them to SOD1 variants. Most of the previously reported variants have been reclassified as likely pathogenic and pathogenic based on the modified weight of the PS3 criterion, highlighting how in vivo or in vitro functional studies are determining their interpretation and classification. Furthermore, this study reveals the concordance and discordance of annotations between open databases, indicating the need for expert review to adapt the study of variants to a specific disease. Indeed, in complex diseases, such as ALS, the oligogenic inheritance, the presence of genes that act as risk factors and the reduced penetration must be considered. Overall, the diagnosis of ALS remains clinical, and improving variant classification could support genetic data as diagnostic criteria. Full article

(This article belongs to the Special Issue Functional Studies for Interpreting Genetic Variants Associated with Genetic Disorders)

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10 pages, 1459 KiB

Open AccessArticle

Possible Catch-Up Developmental Trajectories for Children with Mild Developmental Delay Caused by NAA15 Pathogenic Variants

by Yu Tian, Hua Xie, Shenghai Yang, Shaofang Shangguan, Jianhong Wang, Chunhua Jin, Yu Zhang, Xiaodai Cui, Yanyu Lyu, Xiaoli Chen and Lin Wang

Genes 2022, 13(3), 536; https://doi.org/10.3390/genes13030536 - 18 Mar 2022

Cited by 7 | Viewed by 3379

Abstract

Variants in NAA15 are closely related to neurodevelopmental disorders (NDDs). In this study, we investigated the spectrum and clinical features of NAA15 variants in a Chinese NDD cohort of 769 children. Four novel NAA15 pathogenic variants were detected by whole-exome sequencing, including three [...] Read more.

Variants in NAA15 are closely related to neurodevelopmental disorders (NDDs). In this study, we investigated the spectrum and clinical features of NAA15 variants in a Chinese NDD cohort of 769 children. Four novel NAA15 pathogenic variants were detected by whole-exome sequencing, including three de novo variants and one maternal variant. The in vitro minigene splicing assay confirmed one noncanonical splicing variant (c.1410+5G>C), which resulted in abnormal mRNA splicing. All affected children presented mild developmental delay, and catch-up trajectories were noted in three patients based on their developmental scores at different ages. Meanwhile, the literature review also showed that half of the reported patients with NAA15 variants presented mild/moderate developmental delay or intellectual disability, and possible catch-up sign was indicated for three affected patients. Taken together, our study expanded the spectrum of NAA15 variants in NDD patients. The affected patients presented mild developmental delay, and possible catch-up developmental trajectories were suggested. Studying the natural neurodevelopmental trajectories of NDD patients with pathogenic variants and their benefits from physical rehabilitations are needed in the future for precise genetic counseling and clinical management. Full article

(This article belongs to the Special Issue Genetic Basis Underlying Neuropsychiatric Disorders)

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17 pages, 2418 KiB

Open AccessEditor’s ChoiceArticle

Characterization of Accessible Chromatin Regions in Cattle Rumen Epithelial Tissue during Weaning

by Clarissa Boschiero, Yahui Gao, Ransom L. Baldwin VI, Li Ma, George E. Liu and Cong-Jun Li

Genes 2022, 13(3), 535; https://doi.org/10.3390/genes13030535 - 18 Mar 2022

Cited by 4 | Viewed by 2824

Abstract

Weaning in ruminants is characterized by the transition from a milk-based diet to a solid diet, which drives a critical gastrointestinal tract transformation. Understanding the regulatory control of this transformation during weaning can help to identify strategies to improve rumen health. This study [...] Read more.

Weaning in ruminants is characterized by the transition from a milk-based diet to a solid diet, which drives a critical gastrointestinal tract transformation. Understanding the regulatory control of this transformation during weaning can help to identify strategies to improve rumen health. This study aimed to identify regions of accessible chromatin in rumen epithelial tissue in pre- and post-weaning calves and investigate differentially accessible regions (DARs) to uncover regulatory elements in cattle rumen development using the ATAC-seq approach. A total of 126,071 peaks were identified, covering 1.15% of the cattle genome. From these accessible regions, 2766 DARs were discovered. Gene ontology enrichment resulted in GO terms related to the cell adhesion, anchoring junction, growth, cell migration, motility, and morphogenesis. In addition, putative regulatory canonical pathways were identified (TGFβ, integrin-linked kinase, integrin signaling, and regulation of the epithelial–mesenchymal transition). Canonical pathways integrated with co-expression results showed that TGFβ and ILK signaling pathways play essential roles in rumen development through the regulation of cellular adhesions. In this study, DARs during weaning were identified, revealing enhancers, transcription factors, and candidate target genes that represent potential biomarkers for the bovine rumen development, which will serve as a molecular tool for rumen development studies. Full article

(This article belongs to the Special Issue Gene Regulation of Development and Reproduction in Mammals)

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16 pages, 4186 KiB

Open AccessArticle

Identification of Genetic Risk Factors of Severe COVID-19 Using Extensive Phenotypic Data: A Proof-of-Concept Study in a Cohort of Russian Patients

by Sergey G. Shcherbak, Anton I. Changalidi, Yury A. Barbitoff, Anna Yu. Anisenkova, Sergei V. Mosenko, Zakhar P. Asaulenko, Victoria V. Tsay, Dmitrii E. Polev, Roman S. Kalinin, Yuri A. Eismont, Andrey S. Glotov, Evgeny Y. Garbuzov, Alexander N. Chernov, Olga A. Klitsenko, Mikhail O. Ushakov, Anton E. Shikov, Stanislav P. Urazov, Vladislav S. Baranov and Oleg S. Glotov

Genes 2022, 13(3), 534; https://doi.org/10.3390/genes13030534 - 17 Mar 2022

Cited by 5 | Viewed by 3780

Abstract

The COVID-19 pandemic has drawn the attention of many researchers to the interaction between pathogen and host genomes. Over the last two years, numerous studies have been conducted to identify the genetic risk factors that predict COVID-19 severity and outcome. However, such an [...] Read more.

The COVID-19 pandemic has drawn the attention of many researchers to the interaction between pathogen and host genomes. Over the last two years, numerous studies have been conducted to identify the genetic risk factors that predict COVID-19 severity and outcome. However, such an analysis might be complicated in cohorts of limited size and/or in case of limited breadth of genome coverage. In this work, we tried to circumvent these challenges by searching for candidate genes and genetic variants associated with a variety of quantitative and binary traits in a cohort of 840 COVID-19 patients from Russia. While we found no gene- or pathway-level associations with the disease severity and outcome, we discovered eleven independent candidate loci associated with quantitative traits in COVID-19 patients. Out of these, the most significant associations correspond to rs1651553 in MYH14p = 1.4 × 10⁻⁷), rs11243705 in SETX (p = 8.2 × 10⁻⁶), and rs16885 in ATXN1 (p = 1.3 × 10⁻⁵). One of the identified variants, rs33985936 in SCN11A, was successfully replicated in an independent study, and three of the variants were found to be associated with blood-related quantitative traits according to the UK Biobank data (rs33985936 in SCN11A, rs16885 in ATXN1, and rs4747194 in CDH23). Moreover, we show that a risk score based on these variants can predict the severity and outcome of hospitalization in our cohort of patients. Given these findings, we believe that our work may serve as proof-of-concept study demonstrating the utility of quantitative traits and extensive phenotyping for identification of genetic risk factors of severe COVID-19. Full article

(This article belongs to the Topic Big Data in Healthcare, Bioinformatics and Precision Medicine)

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18 pages, 20774 KiB

Open AccessArticle

Circum-Saharan Prehistory through the Lens of mtDNA Diversity

by Mame Yoro Diallo, Martina Čížková, Iva Kulichová, Eliška Podgorná, Edita Priehodová, Jana Nováčková, Veronica Fernandes, Luísa Pereira and Viktor Černý

Genes 2022, 13(3), 533; https://doi.org/10.3390/genes13030533 - 17 Mar 2022

Cited by 5 | Viewed by 5736

Abstract

African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid [...] Read more.

African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions. Full article

(This article belongs to the Special Issue The Impact of Ancestry on the Human Genome and Phenome)

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11 pages, 781 KiB

Open AccessEditor’s ChoiceArticle

Are Roma People Descended from the Punjab Region of Pakistan: A Y-Chromosomal Perspective

by Atif Adnan, Allah Rakha, Hayder Lazim, Shahid Nazir, Wedad Saeed Al-Qahtani, Maha Abdullah Alwaili, Sibte Hadi and Chuan-Chao Wang

Genes 2022, 13(3), 532; https://doi.org/10.3390/genes13030532 - 17 Mar 2022

Cited by 4 | Viewed by 6897

Abstract

Gypsies are a separate ethnic group living in Pakistan and some other countries as well. They are mostly known as ‘Roma’ and ‘untouchables’. They have different types of lifestyles as compared to other common people, as they always keep migrating from one place [...] Read more.

Gypsies are a separate ethnic group living in Pakistan and some other countries as well. They are mostly known as ‘Roma’ and ‘untouchables’. They have different types of lifestyles as compared to other common people, as they always keep migrating from one place to another. They do not have proper houses; they live in tent houses and most probably work on daily wages to earn their living. Gypsies cannot be specified according to the place of residence and can only be classified according to their migration route. Previous historical and linguistic research showed the north Indian origin of Roma people. The present study collected 285 unrelated Roma individuals living in Punjab and typed with the Goldeneye Y20 system. Allelic frequencies ranged between 0.0035 and 0.5266, with haplotype diversity (HD) of 0.9999 and discrimination capacity (DC) of 0.8790. Gene diversity (GD) ranged from 0.6489 (DYS391) to 0.9764 (DYS391) (DY385ab). A total of 223 unique alleles were observed. Interestingly, the haplogroup R accounted for 40.56% and J for 22.06%. In MDS analysis, Pakistani Roma formed a close cluster with Roma from Constanta, Romania. The migration pattern of the Roma population from Pakistan, India and Europe was inferred using coalescence theory in the Migrate-n program. Overlapping Y-STR data were used to test different migration models. These migration models showed us the dominant gene flow from Pakistan to India and Europe to Pakistan. The results of our study showed that Y STRs provided substantially stronger discriminatory power in the Pakistani Roma population. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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11 pages, 1392 KiB

Open AccessArticle

Identification of Endosymbiotic Virus in Small Extracellular Vesicles Derived from Trichomonas vaginalis

by Seow-Chin Ong, Wei-Hung Cheng, Fu-Man Ku, Chih-Yu Tsai, Po-Jung Huang, Chi-Ching Lee, Yuan-Ming Yeh, Petr Rada, Ivan Hrdý, Ravi Kumar Narayanasamy, Tamara Smutná, Rose Lin, Hong-Wei Luo, Cheng-Hsun Chiu, Jan Tachezy and Petrus Tang

Genes 2022, 13(3), 531; https://doi.org/10.3390/genes13030531 - 17 Mar 2022

Cited by 10 | Viewed by 3225

Abstract

Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in the pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown that extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate the immune response in human vaginal [...] Read more.

Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in the pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown that extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate the immune response in human vaginal epithelial cells and animal models. These results prompted us to examine whether EVs released from TVV+ isolates contained TVV. We isolated small extracellular vesicles (sEVs) from six T. vaginalis isolates that were either TVV free (ATCC 50143), harbored a single (ATCC 30236, ATCC 30238, T1), two (ATCC PRA-98), or three TVV subspecies (ATCC 50148). The presence of TVV subspecies in the six isolates was observed using reverse transcription-polymerase chain reaction (RT-PCR). Transmission electron microscopy (TEM) confirmed the presence of cup-shaped sEVs with a size range from 30–150 nm. Trichomonas vaginalis tetraspanin (TvTSP1; TVAG_019180), the classical exosome marker, was identified in all the sEV preparations. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that all the sEVs isolated from TVV+ isolates contain viral capsid proteins derived from the same TVV subspecies in that isolate as demonstrated by RT-PCR. To provide more comprehensive information on the TVV subspecies population in other T. vaginalis isolates, we investigated the distribution of TVV subspecies in twenty-four isolates by mining the New-Generation Sequencing (NGS) RNAseq datasets. Our results should be beneficial for future studies investigating the role of TVV on the pathogenicity of T. vaginalis and the possible transmission of virus subspecies among different isolates via sEVs. Full article

(This article belongs to the Special Issue Parasite Omics: Applications, Tools and Databases)

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16 pages, 3626 KiB

Open AccessArticle

Identification of Potential Diagnostic Biomarkers and Biological Pathways in Hypertrophic Cardiomyopathy Based on Bioinformatics Analysis

by Tingyan Yu, Zhaoxu Huang and Zhaoxia Pu

Genes 2022, 13(3), 530; https://doi.org/10.3390/genes13030530 - 17 Mar 2022

Cited by 12 | Viewed by 3879

Abstract

Hypertrophic cardiomyopathy (HCM) is a genetic heterogeneous disorder and the main cause of sudden cardiac death in adolescents and young adults. This study was aimed at identifying potential diagnostic biomarkers and biological pathways to help to diagnose and treat HCM through bioinformatics analysis. [...] Read more.

Hypertrophic cardiomyopathy (HCM) is a genetic heterogeneous disorder and the main cause of sudden cardiac death in adolescents and young adults. This study was aimed at identifying potential diagnostic biomarkers and biological pathways to help to diagnose and treat HCM through bioinformatics analysis. We selected the GSE36961 dataset from the Gene Expression Omnibus (GEO) database and identified 893 differentially expressed genes (DEGs). Subsequently, 12 modules were generated through weighted gene coexpression network analysis (WGCNA), and the turquoise module showed the highest negative correlation with HCM (cor = −0.9, p-value = 4 × 10⁻⁵²). With the filtering standard gene significance (GS) < −0.7 and module membership (MM) > 0.9, 19 genes were then selected to establish the least absolute shrinkage and selection operator (LASSO) model, and LYVE1, MAFB, and MT1M were finally identified as key genes. The expression levels of these genes were additionally verified in the GSE130036 dataset. Gene Set Enrichment Analysis (GSEA) showed oxidative phosphorylation, tumor necrosis factor alpha-nuclear factor-κB (TNFα-NFκB), interferon-gamma (IFNγ) response, and inflammatory response were four pathways possibly related to HCM. In conclusion, LYVE1, MAFB, and MT1M were potential biomarkers of HCM, and oxidative stress, immune response as well as inflammatory response were likely to be associated with the pathogenesis of HCM. Full article

(This article belongs to the Special Issue Transcriptomics and Bioinformatics in Precision Medicine)

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23 pages, 2614 KiB

Open AccessEditor’s ChoiceReview

An Expanding Toolkit for Heterochromatin Repair Studies

by Chetan C. Rawal, Nadejda L. Butova, Anik Mitra and Irene Chiolo

Genes 2022, 13(3), 529; https://doi.org/10.3390/genes13030529 - 17 Mar 2022

Cited by 4 | Viewed by 3483

Abstract

Pericentromeric heterochromatin is mostly composed of repetitive DNA sequences prone to aberrant recombination. Cells have developed highly specialized mechanisms to enable ‘safe’ homologous recombination (HR) repair while preventing aberrant recombination in this domain. Understanding heterochromatin repair responses is essential to understanding the critical [...] Read more.

Pericentromeric heterochromatin is mostly composed of repetitive DNA sequences prone to aberrant recombination. Cells have developed highly specialized mechanisms to enable ‘safe’ homologous recombination (HR) repair while preventing aberrant recombination in this domain. Understanding heterochromatin repair responses is essential to understanding the critical mechanisms responsible for genome integrity and tumor suppression. Here, we review the tools, approaches, and methods currently available to investigate double-strand break (DSB) repair in pericentromeric regions, and also suggest how technologies recently developed for euchromatin repair studies can be adapted to characterize responses in heterochromatin. With this ever-growing toolkit, we are witnessing exciting progress in our understanding of how the ‘dark matter’ of the genome is repaired, greatly improving our understanding of genome stability mechanisms. Full article

(This article belongs to the Special Issue DNA Damage Response Mechanisms in Model Systems)

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8 pages, 243 KiB

Open AccessEditor’s ChoiceCommentary

Phenotypic Variability in Phelan–McDermid Syndrome and Its Putative Link to Environmental Factors

by Luigi Boccuto, Andrew Mitz, Ludovico Abenavoli, Sara M. Sarasua, William Bennett, Curtis Rogers, Barbara DuPont and Katy Phelan

Genes 2022, 13(3), 528; https://doi.org/10.3390/genes13030528 - 17 Mar 2022

Cited by 5 | Viewed by 2479

Abstract

Phelan–McDermid syndrome (PMS) is a multi-systemic disorder characterized by both genetic and phenotypic variability. Genetic abnormalities causing PMS span from pathogenic variants of the SHANK3 gene to chromosomal rearrangements affecting the 22q13 region and leading to the loss of up to over nine [...] Read more.

Phelan–McDermid syndrome (PMS) is a multi-systemic disorder characterized by both genetic and phenotypic variability. Genetic abnormalities causing PMS span from pathogenic variants of the SHANK3 gene to chromosomal rearrangements affecting the 22q13 region and leading to the loss of up to over nine megabases. The clinical presentation of individuals with PMS includes intellectual disability, neonatal hypotonia, delayed or absent speech, developmental delay, and minor dysmorphic facial features. Several other features may present with differences in age of onset and/or severity: seizures, autism, regression, sleep disorders, gastrointestinal problems, renal disorders, dysplastic toenails, and disrupted thermoregulation. Among the causes of this phenotypic variability, the size of the 22q13 deletion has effects that may be influenced by environmental factors interacting with haploinsufficiency or hemizygous variants of certain genes. Another mechanism linking environmental factors and phenotypic variability in PMS involves the loss of one copy of genes like BRD1 or CYP2D6, located at 22q13 and involved in the regulation of genomic methylation or pharmacokinetics, which are also influenced by external agents, such as diet and drugs. Overall, several non-mutually exclusive genetic and epigenetic mechanisms interact with environmental factors and may contribute to the clinical variability observed in individuals with PMS. Characterization of such factors will help to better manage this disorder. Full article

(This article belongs to the Special Issue Gene-Exposome Interactions in Mental Illness)

23 pages, 1904 KiB

Open AccessReview

PTCHD1: Identification and Neurodevelopmental Contributions of an Autism Spectrum Disorder and Intellectual Disability Susceptibility Gene

by Stephen F. Pastore, Sangyoon Y. Ko, Paul W. Frankland, Paul A. Hamel and John B. Vincent

Genes 2022, 13(3), 527; https://doi.org/10.3390/genes13030527 - 17 Mar 2022

Cited by 8 | Viewed by 4878

Abstract

Over the last one and a half decades, copy number variation and whole-genome sequencing studies have illuminated the considerable genetic heterogeneity that underlies the etiologies of autism spectrum disorder (ASD) and intellectual disability (ID). These investigations support the idea that ASD may result [...] Read more.

Over the last one and a half decades, copy number variation and whole-genome sequencing studies have illuminated the considerable genetic heterogeneity that underlies the etiologies of autism spectrum disorder (ASD) and intellectual disability (ID). These investigations support the idea that ASD may result from complex interactions between susceptibility-related genetic variants (single nucleotide variants or copy number variants) and the environment. This review outlines the identification and neurobiological characterization of two such genes located in Xp22.11, Patched domain-containing 1 (PTCHD1), and its antisense lncRNA PTCHD1-AS. Animal models of Ptchd1 disruption have recapitulated a subset of clinical symptoms related to ASD as well as to ID. Furthermore, these Ptchd1 mouse knockout studies implicate the expression of Ptchd1 in both the thalamic and the hippocampal brain regions as being crucial for proper neurodevelopment and cognitive function. Altered kynurenine metabolic signalling has been postulated as a disease mechanism in one of these animal studies. Additionally, ASD patient-derived induced pluripotent stem cells (iPSCs) carrying a copy number loss impacting the antisense non-coding RNA PTCHD1-AS have been used to generate 2D neuronal cultures. While copy number loss of PTCHD1-AS does not affect the transcription of PTCHD1, the neurons exhibit diminished miniature excitatory postsynaptic current frequency, supporting its role in ASD etiology. A more thorough understanding of risk factor genes, such as PTCHD1 and PTCHD1-AS, will help to clarify the intricate genetic and biological mechanisms that underlie ASD and ID, providing a foundation for meaningful therapeutic interventions to enhance the quality of life of individuals who experience these conditions. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Subtypes of Autism Spectrum Disorder)

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