Identification and Splicing Characterization of Novel TMC6 and TMC8 Variants Associated With Epidermodysplasia Verruciformis in Three Chinese Families
Conclusion: We identified three novel disease-causing variants in TMC6 or TMC8 in three Chinese families with EV. The EV phenotypes of the three patients were due to a reduction in TMC6 or TMC8. Our findings expand the genetic causes of EV in the Chinese population. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil
Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a gen...
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

Long Non-coding RNA: An Emerging Contributor and Potential Therapeutic Target in Renal Fibrosis
Renal fibrosis (RF) is a pathological process that culminates in terminal renal failure in chronic kidney disease (CKD). Fibrosis contributes to progressive and irreversible decline in renal function. However, the molecular mechanisms involved in RF are complex and remain poorly understood. Long non-coding RNAs (lncRNAs) are a major type of non-coding RNAs, which significantly affect various disease processes, cellular homeostasis, and development through multiple mechanisms. Recent investigations have implicated aberrantly expressed lncRNA in RF development and progression, suggesting that lncRNAs play a crucial role in d...
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

MEF2C Common Genetic Variation Is Associated With Different Aspects of Cognition in Non-Hispanic White and Caribbean Hispanic Non-demented Older Adults
DiscussionMEF2C variant-cognitive associations shed light on an apparent role for MEF2C in both memory and non-memory aspects of cognition in individuals from NHW and CH ancestries. However, the little overlap in the specific SNP-cognition associations in CH versus NHW highlights the differences in genetic architectural variations among those from different ancestries that should be considered while studying the MEF2C gene. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

Genome-Wide Identification and Characterization of the Potato IQD Family During Development and Stress
This study presents a comprehensive overview of the potato IQD gene family and lays a foundation for further analysis of the StIQDs functions in plant development and stress response. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

Intercellular Adhesion Molecule-1 Gene Polymorphisms and Susceptibility to Cervical Cancer in the Northern Chinese Han Population
Many epidemiological studies have confirmed that ICAM-1 gene single-nucleotide polymorphisms (SNPs) are associated with susceptibility of various cancers, but there are relatively few studies on the relationship between ICAM-1 gene polymorphisms and the risk of cervical cancer. Therefore, we aimed to explore the potential role of ICAM-1 gene polymorphisms and the combined effect of SNPs in the pathogenesis of cervical cancer in Han women in northern China. This case–control group includes 488 cases of cervical cancer, 684 cases of cervical precancerous lesions, and 510 healthy females. Multiplex polymerase chain reac...
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

Predictive Biomarkers of Dicycloplatin Resistance or Susceptibility in Prostate Cancer
ConclusionWe successfully used cfDNA to monitor mutational profiles of PCa and designed an effective composite marker to select patients for dicycloplatin treatment based on their mutational profile. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly...
Source: Frontiers in Genetics - July 27, 2021 Category: Genetics & Stem Cells Source Type: research

Comprehensive Analysis of the Expression Characteristics of the Enhancer of the Zeste Homolog 2 Gene in Pan-Cancer
Although more and more studies have shown that EZH2 was closely related to human cancer, no pan-cancer analysis is available. Therefore, we summarized and analyzed the potential carcinogenic effect of EZH2 for the first time based on TCGA (cancer genome map) datasets. EZH2 is expressed highly in most tumors and there is a significant correlation between the EZH2 expression and the prognosis of patients. We observed the increased phosphorylation levels of T487 in breast cancer, colon cancer, UCEC, and LUAD. The expression of EZH2 was associated with the CD8+, tregs, macrophage, and cancer-associated fibroblast infiltration ...
Source: Frontiers in Genetics - July 26, 2021 Category: Genetics & Stem Cells Source Type: research

ARG2, MAP4K5 and TSTA3 as Diagnostic Markers of Steroid-Induced Osteonecrosis of the Femoral Head and Their Correlation With Immune Infiltration
ConclusionARG2, MAP4K5, and TSTA3 are potential diagnostic genes for SONFH, and infiltration of immune cells may critically impact SONFH occurrence and progression. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 26, 2021 Category: Genetics & Stem Cells Source Type: research

Causal Relationship Between Parathyroid Hormone and the Risk of Osteoarthritis: A Mendelian Randomization Study
BackgroundPrevious studies have demonstrated an inverse association between parathyroid hormone (PTH) and the risk of osteoarthritis (OA). However, it remains unknown whether such association reflects causality. We aimed to apply a Mendelian randomization (MR) approach to investigate the causal association between PTH and OA.Materials and MethodsWe performed a two-sample MR analysis using summary statistics from 13 cohorts (PTH, N = 29,155) and a recent genome-wide association study meta-analysis (OA, N = 455,221) by the UK Biobank and Arthritis Research UK OA Genetics (arcOGEN). MR analyses were carried out mainly using t...
Source: Frontiers in Genetics - July 26, 2021 Category: Genetics & Stem Cells Source Type: research

The Potential of Serum Exosomal hsa_circ_0028861 as the Novel Diagnostic Biomarker of HBV-Derived Hepatocellular Cancer
Hepatitis B virus (HBV)-derived hepatocellular cancer (HCC) is a serious threat to human health, especially in China. There is no highly sensitive and specific HCC biomarker at present, which makes it difficult to detect HCC at the early stage. Serum exosomal circular RNAs (circRNAs) have been reported as novel diagnostic and prognostic biomarkers of cancers. In the present study, we aimed to explore the diagnostic performance of serum exosomal circRNAs for HBV-derived HCC screening. At first, many circRNAs were found to be differentially expressed in the serum exosomes of HCC individuals by microarray analysis. The valida...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel Multi-Exon Deletion of PACS1 in a Three-Generation Pedigree: Supplements to PACS1 Neurodevelopmental Disorder Spectrum
This study might supplement the spectrum of PACS1-NDD and demonstrates that the loss of function variation in PACS1 displays no contributions to the typical SHMS which is caused by the recurrent c.607C> T (p.Arg203Trp) variant. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs
This study generated a valuable dataset of H3K4me3 and H3K27ac regions in porcine pituitary glands and revealed H3K4me3 and H3K27ac peaks with differential activity between Bama Xiang and Large White pigs. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Predicting Protein Therapeutic Candidates for Bovine Babesiosis Using Secondary Structure Properties and Machine Learning
This study investigates the novel use of protein secondary structure characteristics and machine learning algorithms to predict exportome membership probabilities. The premise of the approach is to detect characteristic differences that can help classify one protein type from another. Structural properties such as a protein’s local conformational classification states, backbone torsion angles ϕ (phi) and ψ (psi), solvent-accessible surface area, contact number, and half-sphere exposure are explored here as potential distinguishing protein characteristics. The presented methods that exploit these structural prope...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

The CPNE Family and Their Role in Cancers
Lung cancer is the leading cause of cancer-related deaths worldwide. Despite significant advances in cancer research and treatment, the overall prognosis of lung cancer patients remains poor. Therefore, the identification for novel therapeutic targets is critical for the diagnosis and treatment of lung cancer. CPNEs (copines) are a family of membrane-bound proteins that are highly conserved, soluble, ubiquitous, calcium dependent in a variety of eukaryotes. Emerging evidences have also indicated CPNE family members are involved in cancer development and progression as well. However, the expression patterns and clinical rol...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Construction of Circulating MicroRNAs-Based Non-invasive Prediction Models of Recurrent Implantation Failure by Network Analysis
ConclusionThe stability and non-invasiveness of the circular miRNA prediction model provided a new method for diagnosis in RIF patients. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Metabolomics in the Diagnosis and Prognosis of COVID-19
Coronavirus disease 2019 (COVID-19) pandemic triggered an unprecedented global effort in developing rapid and inexpensive diagnostic and prognostic tools. Since the genome of SARS-CoV-2 was uncovered, detection of viral RNA by RT-qPCR has played the most significant role in preventing the spread of the virus through early detection and tracing of suspected COVID-19 cases and through screening of at-risk population. However, a large number of alternative test methods based on SARS-CoV-2 RNA or proteins or host factors associated with SARS-CoV-2 infection have been developed and evaluated. The application of metabolomics in ...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Editorial: Computational Proteomics and Integration of Data Resources for Advanced Studies in Life Sciences
(Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Genetically Predicted Fibroblast Growth Factor 23 and Major Cardiovascular Diseases, Their Risk Factors, Kidney Function, and Longevity: A Two-Sample Mendelian Randomization Study
ConclusionThis study suggests that genetically predicted higher FGF23 may be protective against CAD and T2DM. Future studies should explore the underlying mechanisms related to the potential protective effect of FGF23. FGF23 was unlikely a cause of poorer renal function. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Investigation of Thermomorphogenesis-Related Genes for a Multi-Silique Trait in Brassica napus by Comparative Transcriptome Analysis
This study paves a way to a new perspective into flower/fruit development in Brassica plants. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Construction of Mode of Action for Cadmium-Induced Renal Tubular Dysfunction Based on a Toxicity Pathway-Oriented Approach
Although it is recognized that cadmium (Cd) causes renal tubular dysfunction, the mechanism of Cd-induced nephrotoxicity is not yet fully understood. Mode of action (MOA) is a developing tool for chemical risk assessment. To establish the mechanistic MOA of Cd-induced renal tubular dysfunction, the Comparative Toxicogenomics Database (CTD) was used to obtain genomics data of Cd-induced nephrotoxicity, and Ingenuity® Pathway Analysis (IPA) software was applied for bioinformatics analysis. Based on the perturbed toxicity pathways during the process of Cd-induced nephrotoxicity, we established the MOA of Cd-induced renal ...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

An Assessment of the Factors Influencing the Prediction Accuracy of Genomic Prediction Models Across Multiple Environments
The effects of climate change create formidable challenges for breeders striving to produce sufficient food quantities in rapidly changing environments. It is therefore critical to investigate the ability of multi-environment genomic prediction (GP) models to predict genomic estimated breeding values (GEBVs) in extreme environments. Exploration of the impact of training set composition on the accuracy of such GEBVs is also essential. Accordingly, we examined the influence of the number of training environments and the use of environmental covariates (ECs) in GS models on four subsets of n = 500 lines of the soybean nested ...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

RESIC: A Tool for Comprehensive Adenosine to Inosine RNA Editing Site Identification and Classification
Adenosine to inosine (A-to-I) RNA editing, the most prevalent type of RNA editing in metazoans, is carried out by adenosine deaminases (ADARs) in double-stranded RNA regions. Several computational approaches have been recently developed to identify A-to-I RNA editing sites from sequencing data, each addressing a particular issue. Here, we present RNA Editing Sites Identification and Classification (RESIC), an efficient pipeline that combines several approaches for the detection and classification of RNA editing sites. The pipeline can be used for all organisms and can use any number of RNA-sequencing datasets as input. RES...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Aqueous Triple-Phase System in Microwell Array for Generating Uniform-Sized DNA Hydrogel Particles
In this study, we demonstrate that single, uniform DNA hydrogel particles can form inside aqueous/aqueous two-phase systems (ATPSs) assembled in a microwell array. In this process, uniform dextran droplets are formed in a microwell array inside a microfluidic device. The dextran droplets, which contain DNA motifs, are isolated from each other by an immiscible PEG solution containing magnesium ions and spermine, which enables the DNA hydrogel to undergo gelation. Upon thermal annealing of the device, we observed the formation of an aqueous triple-phase system in which uniform DNA hydrogel particles (the innermost aqueous ph...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel Germline Compound Heterozygous Mutation of BRCA2 Gene Associated With Familial Peripheral Neuroblastic Tumors in Two Siblings
ConclusionIn summary, these results revealed a novel germline compound heterozygous mutation of the BRCA2 gene associated with familial PNTs. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Genetic Modulation of Initial Sensitivity to Δ9-Tetrahydrocannabinol (THC) Among the BXD Family of Mice
Cannabinoid receptor 1 activation by the major psychoactive component in cannabis, Δ9-tetrahydrocannabinol (THC), produces motor impairments, hypothermia, and analgesia upon acute exposure. In previous work, we demonstrated significant sex and strain differences in acute responses to THC following administration of a single dose (10 mg/kg, i.p.) in C57BL/6J (B6) and DBA/2J (D2) inbred mice. To determine the extent to which these differences are heritable, we quantified acute responses to a single dose of THC (10 mg/kg, i.p.) in males and females from 20 members of the BXD family of inbred strains derived by crossing ...
Source: Frontiers in Genetics - July 23, 2021 Category: Genetics & Stem Cells Source Type: research

Integrated Analysis of Hepatic miRNA and mRNA Expression Profiles in the Spontaneous Reversal Process of Liver Fibrosis
Liver fibrosis results from the imbalance between extracellular matrix (ECM) production and degradation, which is a common pathological consequence of various chronic liver diseases. Although many miRNAs have been reported in liver fibrosis progression, miRNA-mRNA interactions in its reversal process remain to be elucidated. In the current study, we performed an integrated analysis of miRNA and mRNA expression profiles in the mouse model with the spontaneous reversal potency of liver fibrosis. A total of 102 miRNA and 2,845 mRNAs showed significant differential expression in reversal mice compared to fibrotic mice. Moreove...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

Association of NLRP3 rs35829419 and rs10754558 Polymorphisms With Risks of Autoimmune Diseases: A Systematic Review and Meta-Analysis
The existing knowledge about the association between NLRP3 rs35829419/rs10754558 polymorphisms and susceptibility to autoimmune diseases (AIDs) remains controversial. Herein, a meta-analysis was performed to evaluate such association. We searched databases for relevant studies published in English up to February 2021. Stata14 was used to assess the odds ratio (OR). As for NLRP3 rs35829419, no significant association to overall AIDs was found in three genetic models [A vs. C: OR (95%CI) = 0.89 (0.69–1.14); AC vs. CC: 1.00 (0.77–1.30); AA/AC vs. CC: 0.93 (0.71–1.20)]. However, subgroup analysis by disease t...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA
In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine–Pacific subclade was evident, suggesting a Philippine origin of Paci...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

The Added Value of Whole-Exome Sequencing for Anomalous Fetuses With Detailed Prenatal Ultrasound and Postnatal Phenotype
The objective of the study was to explore the added value of whole-exome sequencing (WES) in abnormal fetuses with detailed prenatal ultrasound and postnatal phenotype with normal karyotype and chromosomal microarray analysis (CMA).MethodsParents of fetuses with structural abnormalities by prenatal ultrasound who consented to provide fetal samples were prospectively recruited from January 2017 to December 2019. With aneuploidies or cases with copy number variations (CNVs) excluded, WES was performed for cases with normal karyotype and CMA results. Detailed prenatal ultrasound and postnatal imaging or pathology features wer...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

A Novel de novo Mutation in EBF3 Associated With Hypotonia, Ataxia, and Delayed Development Syndrome in a Chinese Boy
ConclusionTo the best of our knowledge, this is the first report of EBF3 pathogenic mutation which associated with HADDS in the Chinese population. Our results expand the phenotypes and pathogenic mutation spectrum of HADDS, thus potentially facilitating the clinical diagnosis and genetic counseling of HADDS patients. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

Multi-Omics Data Fusion for Cancer Molecular Subtyping Using Sparse Canonical Correlation Analysis
It is now clear that major malignancies are heterogeneous diseases associated with diverse molecular properties and clinical outcomes, posing a great challenge for more individualized therapy. In the last decade, cancer molecular subtyping studies were mostly based on transcriptomic profiles, ignoring heterogeneity at other (epi-)genetic levels of gene regulation. Integrating multiple types of (epi)genomic data generates a more comprehensive landscape of biological processes, providing an opportunity to better dissect cancer heterogeneity. Here, we propose sparse canonical correlation analysis for cancer classification (SC...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

Genomic and Immunologic Correlates of Indoleamine 2,3-Dioxygenase Pathway Expression in Cancer
In this study, we looked for the genomic and immunologic correlates of IDO pathway expression in cancer using the Cancer Genome Atlas (TCGA) dataset. Strong CD8+ T-cell infiltration, high mutation burden, and expression of exogenous viruses [Epstein-Barr virus (EBV), Human papilloma virus (HPV), and Hepatitis C virus (HCV)] or endogenous retrovirus (ERV3-2) were associated with over-expression of IDO-1 in most cancer types, IDO-2 in many cancer types, and TDO-2 in a few cancer types. High mutation burden in ER+ HER2− breast cancer, and ERV3-2 expression in ER− HER2− and HER2+ breast, colon, and endometria...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

Identification and Validation of a Ferroptosis-Related Long Non-coding RNA Signature for Predicting the Outcome of Lung Adenocarcinoma
This study aimed to determine the role of ferroptosis-associated long non-coding RNAs (lncRNAs) in LUAD and to establish a prognostic model.MethodsWe downloaded ferroptosis-related genes from the FerrDb database and RNA sequencing data and clinicopathological characteristics from The Cancer Genome Atlas. We randomly divided the data into training and validation sets. Ferroptosis-associated lncRNA signatures with the lowest Akaike information criteria were determined using COX regression analysis and the least absolute shrinkage and selection operator. The risk scores of ferroptosis-related lncRNAs were calculated, and pati...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

From the Farm to the Lab: How Chicken Embryos Contribute to the Field of Teratology
Congenital anomalies and its causes, particularly, by external factors are the aim of the field called teratology. The external factors studied by teratology are known as teratogens and can be biological or environmental factors for example, chemicals, medications, recreational drugs, environmental pollutants, physical agents (e.g., X-rays and maternal hyperthermia) and maternal metabolic conditions. Proving the teratogenicity of a factor is a difficult task requiring epidemiology studies as well as experimental teratology evidence from the use of animal models, one of which is the chicken embryo. This model in particular ...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

Obesity, Type 2 Diabetes, and the Risk of Carpal Tunnel Syndrome: A Two-Sample Mendelian Randomization Study
In this study we performed a two-sample Mendelian randomization to assess the causal effect of obesity, T2D on the risk of CTS. Single nucleotide polymorphisms associated with the body mass index (BMI) and T2D were extracted from genome-wide association studies. Summary-level results of CTS were available through FinnGen repository. Univariable Mendelian randomization (MR) with inverse-variance-weighted method indicated a positive correlation of BMI with CTS risk [odds ratio (OR) 1.66, 95% confidence interval (CI), 1.39–1.97]. Genetically proxied T2D also significantly increased the risk of CTS [OR 1.17, 95% CI (1.07...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

NMFNA: A Non-negative Matrix Factorization Network Analysis Method for Identifying Modules and Characteristic Genes of Pancreatic Cancer
Pancreatic cancer (PC) is a highly fatal disease, yet its causes remain unclear. Comprehensive analysis of different types of PC genetic data plays a crucial role in understanding its pathogenic mechanisms. Currently, non-negative matrix factorization (NMF)-based methods are widely used for genetic data analysis. Nevertheless, it is a challenge for them to integrate and decompose different types of genetic data simultaneously. In this paper, a non-NMF network analysis method, NMFNA, is proposed, which introduces a graph-regularized constraint to the NMF, for identifying modules and characteristic genes from two-type PC dat...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer
High-throughput technologies do not only provide novel means for basic biological research but also for clinical applications in hospitals. For instance, the usage of gene expression profiles as prognostic biomarkers for predicting cancer progression has found widespread interest. Aside from predicting the progression of patients, it is generally believed that such prognostic biomarkers also provide valuable information about disease mechanisms and the underlying molecular processes that are causal for a disorder. However, the latter assumption has been challenged. In this paper, we study this problem for prostate cancer. ...
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

KCNMB2-AS1 Promotes Bladder Cancer Progression Through Sponging miR-374a-3p to Upregulate S100A10
In conclusion, our results demonstrated that lncRNA KCNMB2-AS1 can promote the progression of bladder cancer through regulation of miR-374a-3p/S100A10. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 22, 2021 Category: Genetics & Stem Cells Source Type: research

A Potential Immune-Related Long Non-coding RNA Prognostic Signature for Ovarian Cancer
In conclusion, our study reveals novel immune-related lncRNAs that may serve as independent prognostic factors in OC. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of Distinct Molecular Subtypes of Endometrioid Adenocarcinoma
In this study, we identified two distinct molecular subtypes of EAC with different gene expression patterns and clinicopathologic characteristics. Subtype I EAC cases, accounting for the majority of cases (56%), were associated with an earlier stage, a more well-differentiated grade, a lower tumor invasion rate, and a more favorable prognosis, and the median tumor necrosis percent (15%) was also significantly higher in subtype I EAC. In contrast, subtype II EAC represents high-grade EAC, with a higher tumor invasion rate and tumor weight. The up-regulated genes in subtype I EAC were associated with the immune response, def...
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

SLC4A11 and MFSD3 Gene Expression Changes in Deoxynivalenol Treated IPEC-J2 Cells
This study explored the role of SLC4A11 and MFSD3 in alleviating DON toxicity and analyzed the DNA methylation changes of these two genes. Viability and cell cycle analysis showed that DON exposure decreased the IPEC-J2 viability (P
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

Identification of Potential Prognostic Biomarkers Associated With Cancerometastasis in Skin Cutaneous Melanoma
Skin cutaneous melanoma (SKCM) is a highly aggressive tumor. The mortality and drug resistance among it are high. Thus, exploring predictive biomarkers for prognosis has become a priority. We aimed to find immune cell-based biomarkers for survival prediction. Here 321 genes were differentially expressed in immune-related groups after ESTIMATE analysis and differential analysis. Two hundred nineteen of them were associated with the metastasis of SKCM via weighted gene co-expression network analysis. Twenty-six genes in this module were hub genes. Twelve of the 26 genes were related to overall survival in SKCM patients. Afte...
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

SYTL3 –SLC22A3 Single-Nucleotide Polymorphisms and Gene–Gene/Environment Interactions on the Risk of Hyperlipidemia
The current study aims to further delineate the associations between the synaptotagmin-like 3 (SYTL3) and solute carrier family 22 member 3 (SLC22A3) single-nucleotide polymorphisms (SNPs) and their haplotypes and gene–gene (G × G)/environment (G × E) interactions on the risk of hyperlipidemia (HLP) in the Maonan and Han ethnic groups. Genotype distribution among the SYTL3–SLC22A3 SNPs in 2,829 individual patients bearing no relationship to each other (Han, 1,436; Maonan, 1,393) was analyzed utilizing next-generation sequencing techniques. The genotype frequencies of the rs6455600, rs2129209, and rs...
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

The Optimal Cutoff Value of Z-scores Enhances the Judgment Accuracy of Noninvasive Prenatal Screening
ConclusionThe Z-score is helpful for the accurate judgment of NIPS results and for clinical prenatal counseling. Especially for T21 and T18, Z-scores have an excellent clinical association, which is superior to that seen with X chromosome aneuploids. In addition, using Z-scores to judge NIPS results offers a certain reference value for XXX and XXY but not for XO. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

Multi-Level Analyses of Genome-Wide Association Study to Reveal Significant Risk Genes and Pathways in Neuromyelitis Optica Spectrum Disorder
BackgroundNeuromyelitis optica spectrum disorder (NMOSD) is an inflammatory disease of the central nervous system and it is understandable that environmental and genetic factors underlie the etiology of NMOSD. However, the susceptibility genes and associated pathways of NMOSD patients who are AQP4-Ab positive and negative have not been elucidated.MethodsSecondary analysis from a NMOSD Genome-wide association study (GWAS) dataset originally published in 2018 (215 NMOSD cases and 1244 controls) was conducted to identify potential susceptibility genes and associated pathways in AQP4-positive and negative NMOSD patients, respe...
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

Circular RNA Circ_0013958 Functions as a Tumor Promoter in Ovarian Cancer by Regulating miR-637/PLXNB2 Axis
Conclusion: Circ_0013958 knockdown impeded OC development through modulating the miR-637/PLXNB2 axis, highlighting a therapeutic target for OC. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage
ConclusionIn all, this study provides a resource for genetic and genomic research under abiotic stress in Pak-choi. (Source: Frontiers in Genetics)
Source: Frontiers in Genetics - July 21, 2021 Category: Genetics & Stem Cells Source Type: research

Large Intronic Deletion of the Fragile Site Gene PRKN Dramatically Lowers Its Fragility Without Impacting Gene Expression
Common chromosomal fragile sites (CFSs) are genomic regions prone to form breaks and gaps on metaphase chromosomes during conditions of replication stress. Moreover, CFSs are hotspots for deletions and amplifications in cancer genomes. Fragility at CFSs is caused by transcription of extremely large genes, which contributes to replication problems. These extremely large genes do not encode large proteins, but the extreme sizes of the genes originate from vast introns. Intriguingly, the intron sizes of extremely large genes are conserved between mammals and birds. Here, we have used reverse genetics to address the function a...
Source: Frontiers in Genetics - July 20, 2021 Category: Genetics & Stem Cells Source Type: research