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13 pages, 2497 KB  
Article
Whole-Genome Resequencing Reveals Population Genetic Structure and Selection Signatures in the Golden Wild Yak
by Jianhua Yu, Wei Cong, Xiuming Li, Lu Wang, Kun Jin and Yuguang Zhang
Diversity 2025, 17(10), 687; https://doi.org/10.3390/d17100687 - 30 Sep 2025
Abstract
The wild yak (Bos mutus) is a flagship species on the Qinghai–Tibet Plateau, possessing significant ecological functions and conservation value. Using single-nucleotide polymorphism markers from whole-genome resequencing, we systematically analyzed golden wild yak (n = 37), common wild yak ( [...] Read more.
The wild yak (Bos mutus) is a flagship species on the Qinghai–Tibet Plateau, possessing significant ecological functions and conservation value. Using single-nucleotide polymorphism markers from whole-genome resequencing, we systematically analyzed golden wild yak (n = 37), common wild yak (n = 106), and domestic yak (Bos grunniens) (n = 20) to characterize the population genetic structure and adaptive selection signals in the golden wild yak. Genetic diversity analyses revealed that the golden wild yak had the lowest nucleotide diversity (π = 0.00148) and the highest inbreeding coefficient (FHom = 0.043). Population structure analyses integrating principal component analysis, phylogenetic tree, and ancestral component clustering indicated that the golden wild yak formed a relatively independent evolutionary lineage. However, its genetic differentiation from sympatric common wild yak population was limited (fixation index = 0.031). Selective sweep analysis identified a set of candidate positively selected genes in the golden wild yak genome associated with key traits and physiological functions, including coat color (TYRP1), hypoxia adaptation (MYH11, POLQ), reproductive function (SLC9C1, SPAG16, CFAP97D1), and immune response (CASP8, PGGT1B, BIRC6). Overall, our study reveals a distinct genetic background and selection signatures in the golden wild yak and provides genomic insights to inform the conservation and management of the wild yak. Full article
(This article belongs to the Special Issue Bison and Beyond: Achievements and Problems in Wildlife Conservation)
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19 pages, 11123 KB  
Article
Establishment and Characterization of Behavioral Changes in the Nuclear Localization Human α-Synuclein Transgenic Mice
by Ziou Wang, Mengchen Wei, Shengtao Fan, Zheli Li, Weihu Long, Haiting Wu, Yiwei Zhang and Zhangqiong Huang
Diseases 2025, 13(8), 261; https://doi.org/10.3390/diseases13080261 - 14 Aug 2025
Viewed by 514
Abstract
Objectives: This study aimed to establish a transgenic mouse model expressing nucleus-localized human α-synuclein (α-syn) to investigate its impact on the central nervous system and behavior and the underlying mechanisms involved. Methods: A nuclear localization sequence (NLS) was added to the end of [...] Read more.
Objectives: This study aimed to establish a transgenic mouse model expressing nucleus-localized human α-synuclein (α-syn) to investigate its impact on the central nervous system and behavior and the underlying mechanisms involved. Methods: A nuclear localization sequence (NLS) was added to the end of the human SNCA (hSNCA) gene. Subsequently, an empty vector and a mammalian lentiviral vector of the hSNCA-NLS were constructed. Transgenic mice were generated via microinjection, with genotyping and protein expression confirmed by PCR and western blotting. Only male mice were used in subsequent behavioral and molecular experiments. Immunofluorescence identified the colocalization of human α-syn with the cell nucleus in mouse brain tissues. Behavioral changes in transgenic mice were assessed using open field, rotarod, and O-maze tests. qPCR and Western blotting detected expression levels of genes and proteins related to inflammation, endoplasmic reticulum stress (ERS), and apoptosis. Bulk RNA sequencing was used to screen for differentially expressed genes and signaling pathways. Results: We successfully constructed a transgenic mouse model expressing human α-syn. Human α-syn was widely expressed in the heart, liver, spleen, kidneys, and brain of the mice, with distinct nuclear localization observed. Behavioral assessments demonstrated that, by 2 months of age, the mice exhibited motor dysfunction alongside astrocyte proliferation and neuroinflammation. At 6 months, the elevated expression of ERS-related genes (ATF6, PERK, and IRE1) and activation of the PERK-Beclin1-LC3II pathway indicated progressive ERS. By 9 months, apoptotic events had occurred, accompanied by significant anxiety-like behaviors. Bulk RNA sequencing further identified key differentially expressed genes, including IL-1α, TNF, PERK, BECLIN, GABA, IL-6α, P53, LC3II, NOS, and SPAG, suggesting their involvement in the observed pathological and behavioral phenotypes. Conclusions: The nuclear localization human α-syn transgenic mice were successfully established. These findings demonstrate that nucleus-localized α-syn induces early motor deficits, which are likely mediated by neuroinflammation, whereas later anxiety-like behaviors may result from ERS-induced apoptosis. This model provides a valuable tool for elucidating the role of nuclear α-syn in Parkinson’s disease and supports further mechanistic and therapeutic research. Full article
(This article belongs to the Special Issue Research Progress in Neurodegenerative Diseases)
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20 pages, 2236 KB  
Article
Unveiling Immune Response Mechanisms in Mpox Infection Through Machine Learning Analysis of Time Series Gene Expression Data
by Qinglan Ma, Xianchao Zhou, Lei Chen, Kaiyan Feng, Yusheng Bao, Wei Guo, Tao Huang and Yu-Dong Cai
Life 2025, 15(7), 1039; https://doi.org/10.3390/life15071039 - 30 Jun 2025
Viewed by 698
Abstract
Monkeypox virus (Mpox) has recently drawn global attention due to outbreaks beyond its traditional endemic regions. Understanding the immune response to Mpox infection is essential for improving disease management and guiding vaccine development. In this study, we used several machine learning algorithms to [...] Read more.
Monkeypox virus (Mpox) has recently drawn global attention due to outbreaks beyond its traditional endemic regions. Understanding the immune response to Mpox infection is essential for improving disease management and guiding vaccine development. In this study, we used several machine learning algorithms to analyze time series gene expression data from macaques infected with Mpox, aiming to uncover key immune-related genes involved in different stages of infection. The dataset covered early infection, late infection, and rechallenge phases. We applied nine feature ranking methods to analyze the feature importance, obtaining nine feature lists. Then, the incremental feature selection method was applied to each list to extract key genes and build efficient prediction models and classification rules for each list. This procedure employed twelve classification algorithms and the Synthetic Minority Oversampling Technique. Key genes—such as CD19, MS4A1, and TLR10—were repeatedly identified from multiple feature lists, and are known to play vital roles in B-cell activation, antibody production, and innate immunity. Furthermore, we identified several novel key genes (HS3ST1, SPAG16, and MTARC2) that have not been reported previously. These findings offer valuable insights into the host immune response and highlight potential molecular targets for monitoring and intervention in Mpox infections. Full article
(This article belongs to the Section Physiology and Pathology)
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21 pages, 2878 KB  
Article
Genomic Analysis of Adaptability and Genetic Structure of Jabal Akhdar Goats: Evidence of Positive Selection in an Indigenous Omani Breed
by Zainab Mohammad, Hussain Bahbahani, Ahmad Alfoudari, Kaadhia Al Kharousi, Al Abeer Al Hamrashdi, Al Ghalya Al Toobi and Mohammad Al Abri
Biology 2025, 14(7), 761; https://doi.org/10.3390/biology14070761 - 25 Jun 2025
Viewed by 694
Abstract
Jabal Akhdar goats, native to Oman’s high-altitude Jabal Akhdar mountain range, are recognized for their high growth rate, remarkable twinning rate, and adaptability to harsh environmental conditions. This study assesses the genetic structure, inbreeding levels, effective population size (Ne), and [...] Read more.
Jabal Akhdar goats, native to Oman’s high-altitude Jabal Akhdar mountain range, are recognized for their high growth rate, remarkable twinning rate, and adaptability to harsh environmental conditions. This study assesses the genetic structure, inbreeding levels, effective population size (Ne), and linkage disequilibrium (LD) of Jabal Akhdar goats while identifying genomic regions under positive selection that may contribute to their environmental adaptation. The SNP genotypes from 72 Jabal Akhdar goats and two desert breeds from Egypt (153 Barki and 60 Saidi) revealed a clear genetic distinction between both groups. Within the Jabal Akhdar goats, genetic differentiation was also identified among the three sampled villages, indicating a village-specific genetic structure. The Jabal Akhdar breed exhibited a moderate level of inbreeding (FROH = 0.16), greater than that of the Barki and Saidi breeds. Additionally, Jabal Akhdar goats displayed greater LD and lower Ne levels compared to the Egyptian breeds. Analysis of runs of homozygosity (ROH) and extended haplotype homozygosity-based statistics (iHS and Rsb) identified 93 genomic regions exhibiting signatures of positive selection (80 from ROH, 5 from iHS, and 8 from Rsb). These regions harbor genes associated with traits essential for environmental adaptability, including hypoxia tolerance (SUCNR1, ANGPTL1, MITF, MTUS2), muscle development and function (MBNL1, ACTC1, CAPN5), fertility (GNRHR, CCNA1, SPAG1), UV radiation resistance (UVRAG, BRCA1), bone development (SOST, MEOX1), and lipid metabolism for energy utilization (DGAT2, G6PC, SUCLG2). The results of this study provide valuable insights for identifying causative variants and haplotypes underlying the Jabal Akhdar goat’s superior adaptability. These findings can guide breeders in designing conservation strategies and improving the productivity of this unique indigenous breed. Full article
(This article belongs to the Section Genetics and Genomics)
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13 pages, 2245 KB  
Article
Mouse SPAG6L, a Key Cytoskeleton Modulator Essential for Male Germ Cell Development, Is Not Required for Sertoli Cell Function
by Tao Li, Wei Li, Cheng Zheng, Jannette M. Dufour, William H. Walker, Shuiqiao Yuan and Zhibing Zhang
Cells 2025, 14(11), 783; https://doi.org/10.3390/cells14110783 - 26 May 2025
Viewed by 706
Abstract
Mouse sperm-associated antigen 6-like (SPAG6L) evolved from SPAG6, the mammalian ortholog of Chlamydomonas PF16, which is localized in the central apparatus of the motile cilia and is essential for ciliary motility. Even though the amino acid sequences of the two SPAG6 proteins are [...] Read more.
Mouse sperm-associated antigen 6-like (SPAG6L) evolved from SPAG6, the mammalian ortholog of Chlamydomonas PF16, which is localized in the central apparatus of the motile cilia and is essential for ciliary motility. Even though the amino acid sequences of the two SPAG6 proteins are highly similar, the two proteins have different biological expression patterns in vivo. No major phenotypes were discovered in the global Spag6 knockout mice. However, the global Spag6l knockout mice demonstrated multiple phenotypes in tissues with and without cilia. Since SPAG6L decorates microtubules and modulates cytoskeleton function, and Sertoli cells have a well-developed microtubule transport network, the potential function of SPAG6L in Sertoli cells was evaluated. The floxed Spag6l mice were crossed with Amh-Cre transgenic mice to inactivate the Spag6l gene specifically in Sertoli cells. Surprisingly, the fertility of the homozygous mutant males was not reduced. The testis size and sperm number and motility showed no significant difference to those of the control mice. Testicular histology also showed normal spermatogenesis. No significant changes were observed in the number of Sertoli cells and blood–testis barrier function. Our study showed that the inactivation of only Spag6l does not affect Sertoli cell function during the first 6 months of life. Full article
(This article belongs to the Special Issue Advances in Spermatogenesis)
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23 pages, 18277 KB  
Article
Novel Core Gene Signature Associated with Inflammation-to-Metaplasia Transition in Influenza A Virus-Infected Lungs
by Innokenty A. Savin, Aleksandra V. Sen’kova, Elena P. Goncharova, Marina A. Zenkova and Andrey V. Markov
Int. J. Mol. Sci. 2024, 25(22), 11958; https://doi.org/10.3390/ijms252211958 - 7 Nov 2024
Viewed by 1712
Abstract
Respiratory infections caused by RNA viruses are a major contributor to respiratory disease due to their ability to cause annual epidemics with profound public health implications. Influenza A virus (IAV) infection can affect a variety of host signaling pathways that initiate tissue regeneration [...] Read more.
Respiratory infections caused by RNA viruses are a major contributor to respiratory disease due to their ability to cause annual epidemics with profound public health implications. Influenza A virus (IAV) infection can affect a variety of host signaling pathways that initiate tissue regeneration with hyperplastic and/or dysplastic changes in the lungs. Although these changes are involved in lung recovery after IAV infection, in some cases, they can lead to serious respiratory failure. Despite being ubiquitously observed, there are limited data on the regulation of long-term recovery from IAV infection leading to normal or dysplastic repair represented by inflammation-to-metaplasia transition in mice or humans. To address this knowledge gap, we used integrative bioinformatics analysis with further verification in vivo to elucidate the dynamic molecular changes in IAV-infected murine lung tissue and identified the core genes (Birc5, Cdca3, Plk1, Tpx2, Prc1. Rrm2, Nusap1, Spag5, Top2a, Mcm5) and transcription factors (E2F1, E2F4, NF-YA, NF-YB, NF-YC) involved in persistent lung injury and regeneration processes, which may serve as gene signatures reflecting the long-term effects of IAV proliferation on the lung. Further analysis of the identified core genes revealed their involvement not only in IAV infection but also in COVID-19 and lung neoplasm development, suggesting their potential role as biomarkers of severe lung disease and its complications represented by abnormal epithelial proliferation and oncotransformation. Full article
(This article belongs to the Special Issue Influenza Viruses: Infection and Genomics)
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17 pages, 3956 KB  
Article
Sperm-Associated Antigen 5 Knockout Reduces Doxorubicin and Docetaxel Resistance in Triple-Negative Breast Cancer MDA-MB-231 and BT549 Cells
by Ji He, Jiawei Li, Yanbiao Liu and Yan Li
Cancers 2024, 16(7), 1269; https://doi.org/10.3390/cancers16071269 - 24 Mar 2024
Viewed by 2810
Abstract
Sperm-associated antigen 5 (SPAG5), also known as Astrin, was previously demonstrated as a biomarker for cellular resistance to major breast cancer therapies, including chemo-, endocrine- and targeted therapy. However, the contribution of SPAG5 to anthracycline- and taxane-based chemotherapy in triple-negative breast cancer (TNBC) [...] Read more.
Sperm-associated antigen 5 (SPAG5), also known as Astrin, was previously demonstrated as a biomarker for cellular resistance to major breast cancer therapies, including chemo-, endocrine- and targeted therapy. However, the contribution of SPAG5 to anthracycline- and taxane-based chemotherapy in triple-negative breast cancer (TNBC) remains controversial. In the present study, the SPAG5 knockout cell model was established by using clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system in MDA-MB-231 and BT549 TNBC cell lines. The knockout of SPAG5 was confirmed on both gene and protein levels using genomic PCR, DNA sequencing and western blotting. The functional loss of SPAG5 was determined by colony-formation assay. SPAG5-regulated doxorubicin- and docetaxel-resistance was assessed by MTT and apoptosis assays. The results indicated that all the SPAG5 knockout MDA-MB-231 and BT549 clones were biallelic, where one allele was replaced by the donor template, and the other allele had the same “T” insertion (indel) adjacent to the cutting sites of gRNAs at the exon 1 boundary, irrespective of the gRNAs and cell lines. The locus of indel interrupted the SPAG5 transcription by damaging the GT-AG mRNA processing rule. Deletion of SPAG5 decreased clonogenicity in both MDA-MB-231 and BT549 cells. SPAG5 was able to regulate the resistance and the drug-induced apoptosis of both doxorubicin and docetaxel. In conclusion, recombinant plasmid-based CRISPR-Cas9 technology can be used to delete the SPAG5 gene in the TNBC cell lines. SPAG5 has an important role in regulating cell proliferation and doxorubicin- and docetaxel-resistance in MDA-MB-231 and BT549 cells. Full article
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17 pages, 4935 KB  
Article
Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail
by Natalia A. Volkova, Michael N. Romanov, Alexandra S. Abdelmanova, Polina V. Larionova, Nadezhda Yu. German, Anastasia N. Vetokh, Alexey V. Shakhin, Ludmila A. Volkova, Alexander A. Sermyagin, Dmitry V. Anshakov, Vladimir I. Fisinin, Darren K. Griffin, Johann Sölkner, Gottfried Brem, John C. McEwan, Rudiger Brauning and Natalia A. Zinovieva
Genes 2024, 15(3), 294; https://doi.org/10.3390/genes15030294 - 25 Feb 2024
Cited by 9 | Viewed by 2308
Abstract
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the [...] Read more.
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement. Full article
(This article belongs to the Special Issue Poultry Genetics and Genomics)
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16 pages, 6915 KB  
Article
Analysis of Chromatin Accessibility and DNA Methylation to Reveal the Functions of Epigenetic Modifications in Cyprinus carpio Gonads
by Mingxi Hou, Qi Wang, Ran Zhao, Yiming Cao, Jin Zhang, Xiaoqing Sun, Shuangting Yu, Kaikuo Wang, Yingjie Chen, Yan Zhang and Jiongtang Li
Int. J. Mol. Sci. 2024, 25(1), 321; https://doi.org/10.3390/ijms25010321 - 25 Dec 2023
Cited by 3 | Viewed by 2376
Abstract
Epigenetic modifications are critical in precisely regulating gene expression. The common carp (Cyprinus carpio) is an economically important fish species, and females exhibit faster growth rates than males. However, the studies related to epigenetic modifications in the common carp gonads are [...] Read more.
Epigenetic modifications are critical in precisely regulating gene expression. The common carp (Cyprinus carpio) is an economically important fish species, and females exhibit faster growth rates than males. However, the studies related to epigenetic modifications in the common carp gonads are limited. In this study, we conducted the Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) and Bisulfite sequencing (BS-seq) to explore the roles of epigenetic modifications in the common carp gonads. We identified 84,207 more accessible regions and 77,922 less accessible regions in ovaries compared to testes, and some sex-biased genes showed differential chromatin accessibility in their promoter regions, such as sox9a and zp3. Motif enrichment analysis showed that transcription factors (TFs) associated with embryonic development and cell proliferation were heavily enriched in ovaries, and the TFs Foxl2 and SF1 were only identified in ovaries. We also analyzed the possible regulations between chromatin accessibility and gene expression. By BS-seq, we identified 2087 promoter differentially methylated genes (promoter-DMGs) and 5264 gene body differentially methylated genes (genebody-DMGs) in CG contexts. These genebody-DMGs were significantly enriched in the Wnt signaling pathway, TGF-beta signaling pathway, and GnRH signaling pathway, indicating that methylation in gene body regions could play an essential role in sex maintenance, just like methylation in promoter regions. Combined with transcriptomes, we revealed that the expression of dmrtb1-like, spag6, and fels was negatively correlated with their methylation levels in promoter regions. Our study on the epigenetic modifications of gonads contributes to elucidating the molecular mechanism of sex differentiation and sex maintenance in the common carp. Full article
(This article belongs to the Special Issue Molecular Advance on Reproduction and Fertility of Aquatic Animals)
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52 pages, 8121 KB  
Article
Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis
by Muttanagouda Giriyappagoudar, Basavaraj Vastrad, Rajeshwari Horakeri and Chanabasayya Vastrad
Biomedicines 2023, 11(12), 3109; https://doi.org/10.3390/biomedicines11123109 - 21 Nov 2023
Cited by 6 | Viewed by 5899
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key [...] Read more.
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein–protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy. Full article
(This article belongs to the Special Issue Biomarkers for Idiopathic Pulmonary Fibrosis)
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15 pages, 743 KB  
Review
Non-Invasive Diagnostics of Male Spermatogenesis from Seminal Plasma: Seminal Proteins
by Michal Ješeta, Anna Pospíšilová, Lenka Mekiňová, Kateřina Franzová, Pavel Ventruba, Eva Lousová, Bartosz Kempisty, Tomáš Oždian, Jana Žáková and Igor Crha
Diagnostics 2023, 13(15), 2468; https://doi.org/10.3390/diagnostics13152468 - 25 Jul 2023
Cited by 14 | Viewed by 3212
Abstract
The compounds of seminal plasma have great potential as biomarkers of male fertility and can be used as a diagnostic tool for types of azoospermia. Azoospermia occurs in approximately 1% of the male population, and for an effective therapy of this form of [...] Read more.
The compounds of seminal plasma have great potential as biomarkers of male fertility and can be used as a diagnostic tool for types of azoospermia. Azoospermia occurs in approximately 1% of the male population, and for an effective therapy of this form of male infertility, it is important to distinguish between obstructive and non-obstructive azoospermia. Proteins in seminal plasma can serve as biomarkers for diagnosing azoospermia. Considering the various types of obstructions, a combination of multiple proteins is advisable for diagnostic purposes. In this context, testicular and epididymal proteins are particularly significant, as they are specific to these tissues and typically absent in ejaculate during most obstructions. A combination of multiple biomarkers is more effective than the analysis of a single protein. This group of markers contains TEX101 and ECM1 proteins, combined detections of these two bring a diagnostic output with a high sensitivity and specificity. Similar results were observed for combined detection of TEX101 and SPAG1. The effective using of specific biomarkers from seminal plasma can significantly improve the existing approaches to diagnosis of the causes of male infertility. Full article
(This article belongs to the Section Pathology and Molecular Diagnostics)
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15 pages, 3809 KB  
Article
SPAG9 Expression Predicts Good Prognosis in Patients with Clear-Cell Renal Cell Carcinoma: A Bioinformatics Analysis with Experimental Validation
by Liwen Qiao, Lu Zhang and Huiming Wang
Genes 2023, 14(4), 944; https://doi.org/10.3390/genes14040944 - 20 Apr 2023
Cited by 3 | Viewed by 2568
Abstract
Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive type of renal-cell carcinoma (RCC). Sperm-associated antigen 9 (SPAG9) has been reported to promote the progression of a variety of tumors and is thus a potential prognostic marker. This study [...] Read more.
Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive type of renal-cell carcinoma (RCC). Sperm-associated antigen 9 (SPAG9) has been reported to promote the progression of a variety of tumors and is thus a potential prognostic marker. This study combined a bioinformatics analysis with an experimental validation, exploring the prognostic value of SPAG9 expression in ccRCC patients and the possible underlying mechanisms. The SPAG9 expression was associated with a poor prognosis in pan-cancer patients, but with a good prognosis and slow tumor progression in ccRCC patients. To explore the underlying mechanism, we investigated the roles of SPAG9 in ccRCC and bladder urothelial carcinoma (BLCA). The latter was chosen for comparison with ccRCC to represent the tumor types in which SPAG9 expression suggests a poor prognosis. The overexpression of SPAG9 increased the expression of autophagy-related genes in 786-O cells but not in HTB-9 cells, and SPAG9 expression was significantly correlated with a weaker inflammatory response in ccRCC but not in BLCA. Through an integrated bioinformatics analysis, we screened out seven key genes (AKT3, MAPK8, PIK3CA, PIK3R3, SOS1, SOS2, and STAT5B) in this study. The correlation between SPAG9 expression and ccRCC prognosis depends on the expression of key genes. Since most of the key genes were PI3K-AKT-pathway members, we used the PI3K agonist 740Y-P to stimulate the 786-O cells, to mimic the effect of key-gene overexpression. Compared with the Ov-SPAG9 786-O cells, the 740Y-P further increased the expression of autophagy-related genes by more than twofold. Moreover, we constructed a nomogram based on SPAG9/key genes and other clinical features, which was proven to have some predictive value. Our study found that SPAG9 expression predicted opposite clinical outcomes in pan-cancer and ccRCC patients, and we speculated that SPAG9 suppresses tumor progression by promoting autophagy and inhibiting inflammatory responses in ccRCC. We further found that some genes might cooperate with SPAG9 to promote autophagy, and that these were highly expressed in the tumor stroma and could be represented by key genes. The SPAG9-based nomogram can help to estimate the long-term prognosis of ccRCC patients, indicating that SPAG9 is a potential prognostic marker for ccRCC. Full article
(This article belongs to the Special Issue Bioinformatics of Disease Genes)
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10 pages, 1464 KB  
Communication
Electrostatic Complementarities of Glioblastoma-Resident T-Cell Receptors and Cancer Testis Antigens Linked to Poor Outcomes and High Levels of Sphingosine Kinase-2 Expression
by Miguel A. Arias, Konrad J. Cios, Dorottya B. Kacsoh, Bailey E. Montgomery, Joanna J. Song, Anishaa R. Patel, Andrea Chobrutskiy, Boris I. Chobrutskiy and George Blanck
Biology 2023, 12(4), 575; https://doi.org/10.3390/biology12040575 - 10 Apr 2023
Cited by 3 | Viewed by 1934
Abstract
Introduction. Glioblastoma (GBM) is the most aggressive primary brain tumor in adults. Despite a growing understanding of glioblastoma pathology, the prognosis remains poor. Methods. In this study, we used a previously extensively benchmarked algorithm to retrieve immune receptor (IR) recombination reads from GBM [...] Read more.
Introduction. Glioblastoma (GBM) is the most aggressive primary brain tumor in adults. Despite a growing understanding of glioblastoma pathology, the prognosis remains poor. Methods. In this study, we used a previously extensively benchmarked algorithm to retrieve immune receptor (IR) recombination reads from GBM exome files available from the cancer genome atlas. The T-cell receptor complementarity determining region-3 (CDR3) amino acid sequences that represent the IR recombination reads were assessed and used for the generation of chemical complementarity scores (CSs) that represent potential binding interactions with cancer testis antigens (CTAs), which is an approach particularly suited to a big data setting. Results. The electrostatic CSs representing the TRA and TRB CDR3s and the CTAs, SPAG9, GAGE12E, and GAGE12F, indicated that an increased electrostatic CS was associated with worse disease-free survival (DFS). We also assessed the RNA expression of immune marker genes, which indicated that a high-level expression of SPHK2 and CIITA genes also correlated with high CSs and worse DFS. Furthermore, apoptosis-related gene expression was revealed to be lower when the TCR CDR3-CTA electrostatic CSs were high. Conclusion. Adaptive IR recombination reads from exome files have the potential to aid in GBM prognoses and may provide opportunities to detect unproductive immune responses. Full article
(This article belongs to the Section Immunology)
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18 pages, 3737 KB  
Article
Effect of Structured Phenolic Lipids with EPA/DHA and Gallic Acid against Metabolic-Associated Fatty Liver Disease (MAFLD) in Mice
by Gretel Dovale-Rosabal, Alejandra Espinosa, Alicia Rodríguez, Andrés Barriga, Alan Palomino-Calderón, Nalda Romero, Rodrigo Hernán Troncoso and Santiago Pedro Aubourg
Molecules 2022, 27(22), 7702; https://doi.org/10.3390/molecules27227702 - 9 Nov 2022
Cited by 8 | Viewed by 2761
Abstract
Obesity is the leading risk factor for developing metabolic (dysfunction)-associated fatty liver disease (MAFLD). The food industry has an essential role in searching for new strategies to improve primary food sources to revert some of the metabolic alterations induced by obesity. There is [...] Read more.
Obesity is the leading risk factor for developing metabolic (dysfunction)-associated fatty liver disease (MAFLD). The food industry has an essential role in searching for new strategies to improve primary food sources to revert some of the metabolic alterations induced by obesity. There is consistent evidence that long-chain polyunsaturated fatty acids (n-3 LCPUFA) belonging to the n-3 series, i.e., eicosapentaenoic (20:5n-3, EPA) and docosahexaenoic (22:6n-3, DHA) acids, could revert some alterations associated with obesity-induced metabolic diseases. A relevant tool is the synthesis of structured acylglycerols (sAG), which include EPA or DHA at the sn-2 position. On the other hand, it has been reported that a crucial role of antioxidants is the reversion of MAFLD. In this work, we studied the effects of new molecules incorporating gallic acid (GA) into EPA/DHA-rich structured lipids. Mice were fed with a high-fat diet (60%) for three months and were then divided into five groups for supplementation with sAG and sAG structured with gallic acid (structured phenolic acylglycerols, sPAG). sPAG synthesis was optimized using a 2²-screening factorial design based on the response surface methodology (RSM). Our results show that treatment of sPAG was effective in decreasing visceral fat, fasting glycemia, fasting insulin, suggesting that this new molecule has a potential use in the reversal of MAFLD-associated alterations. Full article
(This article belongs to the Special Issue Bioactive Lipids in Inflammatory Diseases)
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18 pages, 3282 KB  
Article
Evaluation of Green Silver Nanoparticles Fabricated by Spirulina platensis Phycocyanin as Anticancer and Antimicrobial Agents
by Abel-Fattah Salah Soror, Mai Waled Ahmed, Abdalla E. A. Hassan, Mona Alharbi, Nouf H. Alsubhi, Diana A. Al-Quwaie, Ghadeer I. Alrefaei, Najat Binothman, Majidah Aljadani, Safa H. Qahl, Fatima A. Jaber and Hanan Abdalla
Life 2022, 12(10), 1493; https://doi.org/10.3390/life12101493 - 26 Sep 2022
Cited by 9 | Viewed by 4072
Abstract
Green nanotechnology has attracted attention worldwide, especially in treating cancer and drug-resistant section 6 microbes. This work aims to investigate the anticancer activity of green silver nanoparticles synthesized by Spirulina platensis phycocyanin (SPAgNPs) on two cancer cell lines: Lung cancer cell line (A-549) [...] Read more.
Green nanotechnology has attracted attention worldwide, especially in treating cancer and drug-resistant section 6 microbes. This work aims to investigate the anticancer activity of green silver nanoparticles synthesized by Spirulina platensis phycocyanin (SPAgNPs) on two cancer cell lines: Lung cancer cell line (A-549) and breast cancer cell line (MCF-7), compared to the normal human lung cell line (A138). We also aimed to investigate the bactericidal activity against Staphylococcus aureus ATCC29737, Bacillus cereus ATCC11778, Escherichia coli ATCC8379, and Klebsiella pneumonia, as well as the fungicidal activity against Candida albicans (ATCC6019) and Aspergillus niger. The obtained SPAgNPs were spherical and crystalline with a size of 30 nm and a net charge of −26.32 mV. Furthermore, they were surrounded by active groups responsible for stability. The SPAgNPs scavenged 85% of the DPPH radical with a relative increase of approximately 30% over the extract. The proliferation of cancer cells using the MTT assay clarified that both cancer cells (A-549 and MCF-7) are regularly inhibited as they grow on different concentrations of SPAgNPs. The maximum inhibitory effect of SPAgNPs (50 ppm) reached 90.99 and 89.51% against A-549 and MCF7, respectively. Regarding antimicrobial activity, no inhibition zones occurred in bacterial or fungal strains at low concentrations of SPAgNPs and the aqueous Spirulina platensis extract. However, at high concentrations, inhibition zones, especially SPAgNPs, were more potent for all tested microorganisms than their positive controls, with particular reference to Staphylococcus aureus, since the inhibition zones were 3.2, 3.8, and 4.3 mm, and Bacillus cereus was 2.37 mm when compared to tetracycline (2.33 mm). SPAgNPs have more potent antifungal activity, especially against Aspergillus niger, compared to their positive controls. We concluded that SPAgNPs are powerful agents against oxidative stress and microbial infection. Full article
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