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Genes Jun 2024The identification and expression of germ cells are important for studying sex-related mechanisms in fish. The gene, encoding an ATP-dependent RNA helicase, is...
The identification and expression of germ cells are important for studying sex-related mechanisms in fish. The gene, encoding an ATP-dependent RNA helicase, is recognized as a molecular marker of germ cells and plays a crucial role in germ cell development. , an important freshwater economic fish species in China, shows significant sex dimorphism with the female growing faster than the male. However, the molecular mechanisms underlying these sex differences especially involving in the gene in this fish remain poorly understood. In this work, the gene sequence of (named as ) was obtained through RT-PCR and rapid amplification of cDNA end (RACE), and its expression in embryos and tissues was analyzed using qRT-PCR and an in situ hybridization method. Letrozole (LT) treatment on the larvae fish was also conducted to investigate its influence on the gene. The results revealed that the open reading frame (ORF) of was 1989 bp, encoding 662 amino acids. The SaVasa protein contains 10 conserved domains unique to the DEAD-box protein family, showing the highest sequence identity of 95.92% with that of . In embryos, is highly expressed from the two-cell stage to the blastula stage in early embryos, with a gradually decreasing trend from the gastrula stage to the heart-beating stage. Furthermore, was initially detected at the end of the cleavage furrow during the two-cell stage, later condensing into four symmetrical cell clusters with embryonic development. At the gastrula stage, -positive cells increased and began to migrate towards the dorsal side of the embryo. In tissues, is predominantly expressed in the ovaries, with almost no or lower expression in other detected tissues. Moreover, was expressed in phase I-V oocytes in the ovaries, as well as in spermatogonia and spermatocytes in the testis, implying a specific expression pattern of germ cells. In addition, LT significantly upregulated the expression of in a concentration-dependent manner during the key gonadal differentiation period of the fish. Notably, at 120 dph after LT treatment, expression was the lowest in the testis and ovary of the high concentration group. Collectively, findings from gene structure, protein sequence, phylogenetic analysis, RNA expression patterns, and response to LT suggest that is maternally inherited with conserved features, serving as a potential marker gene for germ cells in , and might participate in LT-induced early embryonic development and gonadal development processes of the fish. This would provide a basis for further research on the application of germ cell markers and the molecular mechanisms of sex differences in .
Topics: Animals; Letrozole; Female; Male; Fish Proteins; DEAD-box RNA Helicases; Catfishes; Gene Expression Regulation, Developmental; Germ Cells; Phylogeny
PubMed: 38927693
DOI: 10.3390/genes15060756 -
Genes Jun 2024Patients with advanced-stage epithelial ovarian cancer (EOC) receive treatment with a poly-ADP ribose-polymerase (PARP) inhibitor (PARPi) as maintenance therapy after...
BACKGROUND
Patients with advanced-stage epithelial ovarian cancer (EOC) receive treatment with a poly-ADP ribose-polymerase (PARP) inhibitor (PARPi) as maintenance therapy after surgery and chemotherapy. Unfortunately, many patients experience disease progression because of acquired therapy resistance. This study aims to characterize epigenetic and genomic changes in cell-free DNA (cfDNA) associated with PARPi resistance.
MATERIALS AND METHODS
Blood was taken from 31 EOC patients receiving PARPi therapy before treatment and at disease progression during/after treatment. Resistance was defined as disease progression within 6 months after starting PARPi and was seen in fifteen patients, while sixteen patients responded for 6 to 42 months. Blood cfDNA was evaluated via Modified Fast Aneuploidy Screening Test-Sequencing System (mFast-SeqS to detect aneuploidy, via Methylated DNA Sequencing (MeD-seq) to find differentially methylated regions (DMRs), and via shallow whole-genome and -exome sequencing (shWGS, exome-seq) to define tumor fractions and mutational signatures.
RESULTS
Aneuploid cfDNA was undetectable pre-treatment but observed in six patients post-treatment, in five resistant and one responding patient. Post-treatment ichorCNA analyses demonstrated in shWGS and exome-seq higher median tumor fractions in resistant (7% and 9%) than in sensitive patients (7% and 5%). SigMiner analyses detected predominantly mutational signatures linked to mismatch repair and chemotherapy. DeSeq2 analyses of MeD-seq data revealed three methylation signatures and more tumor-specific DMRs in resistant than in responding patients in both pre- and post-treatment samples (274 vs. 30 DMRs, 190 vs. 57 DMRs, Χ-test < 0.001).
CONCLUSION
Our genome-wide Next-Generation Sequencing (NGS) analyses in PARPi-resistant patients identified epigenetic differences in blood before treatment, whereas genomic alterations were more frequently observed after progression. The epigenetic differences at baseline are especially interesting for further exploration as putative predictive biomarkers for PARPi resistance.
Topics: Humans; Female; Drug Resistance, Neoplasm; Middle Aged; Ovarian Neoplasms; Poly(ADP-ribose) Polymerase Inhibitors; Epigenesis, Genetic; Aged; DNA Methylation; Carcinoma, Ovarian Epithelial; Adult; Aneuploidy; Genomics
PubMed: 38927686
DOI: 10.3390/genes15060750 -
Genes May 2024Approximately half of the cases of chronic kidney disease (CKD) in childhood are caused by congenital anomalies of the kidney and urinary tract (CAKUT). Specific genes...
Approximately half of the cases of chronic kidney disease (CKD) in childhood are caused by congenital anomalies of the kidney and urinary tract (CAKUT). Specific genes were identified as having significant importance in regard to the underlying genetic factors responsible for the CAKUT phenotype, and in our research, we focused on analyzing and comparing the expression levels of ectodysplasin A2 receptor (EDA2R), protocadherin9 (PCDH9), and TNF receptor-associated factor 7 (TRAF7) proteins in the cortex and medulla of healthy control kidneys during developmental phases 2, 3, and 4. We also performed an analysis of the area percentages of the mentioned proteins in the cortical and medullary sections of healthy embryonic and fetal kidneys compared to those affected by CAKUT, including duplex kidneys (DK), horseshoe kidneys (HK), hypoplastic kidneys (HYP), and dysplastic kidneys (DYS). We found that the CAKUT candidate gene proteins EDA2R, PCDH9, and TRAF7 are all expressed during normal human kidney development stages. In DYS, the expression of EDA2R was higher than in normal kidneys, likely due to EDA2R's role in apoptosis, which was upregulated in specific cases and could possibly contribute to the formation of DYS. The expression of PCDH9 was lower in HK, which can be attributed to the possible role of PCDH9 in cell migration suppression. Decreased PCDH9 expression is linked to increased cell migration, potentially contributing to the development of HK. The level of TRAF7 expression was reduced in all examined kidney disorders compared to normal kidneys, suggesting that this reduction might be attributed to the crucial role of TRAF7 in the formation of endothelium and ciliogenesis, both of which are essential for normal kidney development. Further research is required to ascertain the function of these proteins in both the typical development of the kidney and in CAKUT.
Topics: Humans; Kidney; Vesico-Ureteral Reflux; Cadherins; Urogenital Abnormalities; Protocadherins; Urinary Tract; Gene Expression Regulation, Developmental
PubMed: 38927638
DOI: 10.3390/genes15060702 -
Biomedicines Jun 2024Research has identified fetal risk factors for adult diseases, forming the basis for the Developmental Origins of Health and Disease (DOHaD) hypothesis. DOHaD suggests... (Review)
Review
A Review of Fetal Development in Pregnancies with Maternal Type 2 Diabetes Mellitus (T2DM)-Associated Hypothalamic-Pituitary-Adrenal (HPA) Axis Dysregulation: Possible Links to Pregestational Prediabetes.
Research has identified fetal risk factors for adult diseases, forming the basis for the Developmental Origins of Health and Disease (DOHaD) hypothesis. DOHaD suggests that maternal insults during pregnancy cause structural and functional changes in fetal organs, increasing the risk of chronic diseases like type 2 diabetes mellitus (T2DM) in adulthood. It is proposed that altered maternal physiology, such as increased glucocorticoid (GC) levels associated with a dysregulated hypothalamic-pituitary-adrenal (HPA) axis in maternal stress and T2DM during pregnancy, exposes the fetus to excess GC. Prenatal glucocorticoid exposure reduces fetal growth and programs the fetal HPA axis, permanently altering its activity into adulthood. This programmed HPA axis is linked to increased risks of hypertension, cardiovascular diseases, and mental disorders in adulthood. With the global rise in T2DM, particularly among young adults of reproductive age, it is crucial to prevent its onset. T2DM is often preceded by a prediabetic state, a condition that does not show any symptoms, causing many to unknowingly progress to T2DM. Studying prediabetes is essential, as it is a reversible stage that may help prevent T2DM-related pregnancy complications. The existing literature focuses on HPA axis dysregulation in T2DM pregnancies and its link to fetal programming. However, the effects of prediabetes on HPA axis function, specifically glucocorticoid in pregnancy and fetal outcomes, are not well understood. This review consolidates research on T2DM during pregnancy, its impact on fetal programming via the HPA axis, and possible links with pregestational prediabetes.
PubMed: 38927579
DOI: 10.3390/biomedicines12061372 -
Biomedicines Jun 2024Right dominant arrhythmogenic cardiomyopathy, commonly known as Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC), represents a formidable challenge in... (Review)
Review
Right dominant arrhythmogenic cardiomyopathy, commonly known as Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC), represents a formidable challenge in cardiovascular medicine, as conventional therapies are commonly ineffective in impeding disease progression and the development of end-stage heart failure. Recombinant adeno-associated virus (AAV)-mediated gene therapy presents a promising avenue for targeted therapeutic interventions, potentially revolutionising treatment approaches for ARVC patients. Encouraging results from preclinical studies have sparked optimism about the possibility of curing specific subtypes of ARVC in the near future. This narrative review delves into the dynamic landscape of genetic therapy for ARVC, elucidating its underlying mechanisms and developmental stages, and providing updates on forthcoming trials. Additionally, it examines the hurdles and complexities impeding the successful translation of ARVC genetic therapies into clinical practice. Despite notable scientific advancements, the journey towards implementing genetic therapies for ARVC patients in real-world clinical settings is still in its early phases.
PubMed: 38927558
DOI: 10.3390/biomedicines12061351 -
Biology Jun 2024Rice ( L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages,... (Review)
Review
Rice ( L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change.
PubMed: 38927322
DOI: 10.3390/biology13060442 -
Biology May 2024Cotton is a globally significant economic crop. Brassinosteroids (BRs) are crucial to cotton development. This study systematically analyzed the BR synthase gene family...
Cotton is a globally significant economic crop. Brassinosteroids (BRs) are crucial to cotton development. This study systematically analyzed the BR synthase gene family in four cotton species and identified 60 BR genes: 20 in (), 20 in (), 10 in (), and 10 in (). The analysis was extended to chromosomal localization, evolutionary relationships, domain features, and -regulatory elements in the promoter regions of BR synthase genes. The results showed that the BR synthase genes were evenly distributed across different subgenomes and chromosomes. Bioinformatics analyses revealed high conservation of amino acid sequences, secondary structures, and conserved domains among the subfamily members, which is closely linked to their pivotal roles in the BR biosynthesis pathway. -element distribution analysis of the BR synthase genes further underscored the complexity of BR gene expression regulation, which is influenced by multiple factors, including plant hormones, abiotic stress, and transcription factors. Expression profiling of genes in various cotton tissues and developmental stages highlighted the key roles of and in fiber elongation and initiation, respectively. Protein-protein interactions and transcription factor analyses further elucidated the regulatory mechanisms of GhROT3-1 and GhDET2-1 in cotton growth and development. This study lays a theoretical foundation for understanding the role of the BR signaling pathway in cotton development, facilitating molecular breeding.
PubMed: 38927259
DOI: 10.3390/biology13060380 -
Biomolecules May 2024Normal testicular development ensures the process of spermatogenesis, which is a complex biological process. The sustained high productivity of spermatogenesis...
Normal testicular development ensures the process of spermatogenesis, which is a complex biological process. The sustained high productivity of spermatogenesis throughout life is predominantly attributable to the constant proliferation and differentiation of spermatogonial stem cells (SSCs). The self-renewal and differentiation processes of SSCs are strictly regulated by the SSC niche. Therefore, understanding the developmental pattern of SSCs is crucial for spermatogenesis. The Shaziling pig is a medium-sized indigenous pig breed originating from central China. It is renowned for its superior meat quality and early male sexual maturity. The spermatogenic ability of the boars is of great economic importance to the pig industry. To investigate testicular development, particularly the pattern of SSC development in Shaziling pigs, we used single-cell transcriptomics to identify gene expression patterns in 82,027 individual cells from nine Shaziling pig testes at three key postnatal developmental stages. We generated an unbiased cell developmental atlas of Shaziling pig testicular tissues. We elucidated the complex processes involved in the development of SSCs within their niche in the Shaziling pig. Specifically, we identified potential marker genes and cellular signaling pathways that regulate SSC self-renewal and maintenance. Additionally, we proposed potential novel marker genes for SSCs that could be used for SSC isolation and sorting in Shaziling pigs. Furthermore, by immunofluorescence staining of testicular tissues of different developmental ages using marker proteins (UCHL1 and KIT), the developmental pattern of the spermatogonia of Shaziling pigs was intensively studied. Our research enhances the comprehension of the development of SSCs and provides a valuable reference for breeding Shaziling pigs.
Topics: Animals; Male; Swine; RNA-Seq; Spermatogonia; Testis; Adult Germline Stem Cells; Single-Cell Analysis; Cell Differentiation; Spermatogenesis; Stem Cells; Transcriptome
PubMed: 38927011
DOI: 10.3390/biom14060607 -
BMC Plant Biology Jun 2024Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate...
BACKGROUND
Theobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao.
RESULTS
We describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues.
CONCLUSION
The Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.
Topics: Cacao; Transcriptome; Gene Regulatory Networks; Gene Expression Regulation, Plant; Genes, Plant; Gene Expression Profiling; Organ Specificity
PubMed: 38926852
DOI: 10.1186/s12870-024-05171-9 -
BMC Pediatrics Jun 2024The main cause of growth and development delays remains unknown, but it can occur as an interaction between genetic, environmental, and socio-economic factors.
BACKGROUND
The main cause of growth and development delays remains unknown, but it can occur as an interaction between genetic, environmental, and socio-economic factors.
OBJECTIVE
The aim of the study was to investigate the prevalence and social determinants of growth and developmental delays among children aged under five years in Qazvin, Iran.
METHODS
A cross-sectional study was conducted between January 2019 to December 2020 with participation of 1800 mothers with children aged 4-60 months who were referred to comprehensive health centers in Qazvin city, Iran. Structural and intermediate social determinants of health were assessed including: parents and children socio-demographic characteristics, families' living and economic status, parents' behavioral factors, household food security, mother's general health, and perceived social support. Children's growth was assessed based on their anthropometric assessment and their development was assessed using their age-specific Ages and Stages Questionnaire. Data were analyzed using univariable and multivariable logistic regression models using SPSS software version 24 and Stata version 14.
RESULTS
The prevalence of developmental problems in each domain were 4.28% for personal and social delay, 5.72% for gross motor delay, 6.5% for communication delay, 6.72% for fine motor delay, and 8% for problem-solving delay. The prevalence of weight growth delays was 13.56% and height growth delays was 4.66%. Communication, gross motor, and problem-solving delays were higher among children whose fathers' smoked cigarettes. Fine motor delays were lower among mothers with education status of high school diploma and university degree vs. the under diploma group. Personal and social delay was significantly higher among families with fair economic status and lower among children when their fathers were employed (vs. unemployed). Weight and height growth delays were higher among mothers who had experienced pregnancy complications and household food insecure families, respectively.
CONCLUSION
There are different predictors of growth and developmental delay problems among Iranian children aged under five years including fathers' smoking, families' economic status, and household food insecurity as well as history of mothers' pregnancy complications. The present study's findings can be used to screen for at-risk of growth and developmental delays among children and could help in designing and implementation of timely interventions.
Topics: Humans; Cross-Sectional Studies; Iran; Developmental Disabilities; Child, Preschool; Female; Prevalence; Infant; Male; Growth Disorders; Socioeconomic Factors; Social Determinants of Health; Child Development
PubMed: 38926691
DOI: 10.1186/s12887-024-04880-2