Journal of Applied Genetics最新文献

Placental angiogenesis is a pivotal process for feto-maternal circulation and ensures efficient development of the placenta throughout pregnancy. Many factors during in vitro fertilization and embryo transfer procedures may affect placental gene expression and fetus development. The present study aimed to identify differences in angiogenesis-related gene (VEGFA, FGF2, FLT1, and KDR) expression profiles in placentas after assisted reproductive technology fertilization and natural conception in healthy women. In a case-control study, term placentas were collected from Caucasian women after assisted reproductive technology fertilization (N = 20) and after natural conception in women with uncomplicated pregnancy (N = 9). The mRNA expression in placentas was examined for VEGFA, FGF2, FLT1, and KDR genes by real-time quantitative polymerase chain reaction (RT-qPCR). Group stratification was performed for comparison of investigated genes between the type of embryo transferred (fresh/frozen), place of tissue donation (center/margin), and newborns' gender (male/female). In the ART placentas, significant down-regulation of VEGFA gene (p = 0.016) and up-regulation of FLT1 (p = 0.026) and KDR (p < 0.001) gene receptors were observed. Genes encoding VEGFA receptors were up-regulated in both fresh (ET) and frozen (FET) embryo transfer groups compared to controls. For the FLT1 gene, a statistically significant difference was observed between the frozen embryo transfer group and the controls (p = 0.032). Relative expression of KDR was significantly higher for both embryo transfer groups compared to controls (p < 0.001) and between ET and FET (p = 0.002). No statistically significant differences were observed between placental expression in different places of tissue donation and newborns' gender. We observed differences in the placental expression of VEGFA and its receptors FLT1 and KDR in pregnancies after assisted reproductive technology compared to naturally conceived pregnancies. More research is needed to clarify these alterations that may affect placental development and fetal health.

Oral tongue squamous cell carcinoma (OTSCC) is the most common malignancy type among males across the world. However, analysis of molecular markers could be useful in detecting the early-stage OTSCC, which would allow optimal clinical treatments and prolong the survival rate of patients consequently. The study has the objective of detecting the role of salivary biomarkers based on gene promoter hypermethylation. Sample data from 45 OTSCC and normal groups were analyzed to exhibit the methylation levels of salivary biomarkers (TRH, FHIT, MGMT, p16, and RASSF1A). The specificity and sensitivity analysis of methylation biomarkers was conducted in addition to the receiver operating characteristic (ROC) curve for both early-stage and advanced OTSCC stages. Quantitative data findings showed the perfect sensitivity and specificity for TRH, MGMT, p16, and RASSF1A with 100%, and > 90%, respectively. In addition, the results indicated an inefficient area under curves (> 0.7) for these biomarkers to detect the OTSCC. There were no significant differences observed between TRH and FHIT and p16 and MGMT based on the Wilcoxon signed-rank test. The methylation statuses of genes TRH, RASSF1A, p16, and MGMT might become utilized as predictive biomarkers for clinical application in early diagnosis of OTSCC and noninvasive oral cancer screening.

The Homeobox (HOX) gene family is essential to regulating cellular processes because it maintains the exact coordination required for tissue homeostasis, cellular differentiation, and embryonic development. The most distinctive feature of this class of genes is the presence of the highly conserved DNA region known as the homeobox, which is essential for controlling their regulatory activities. Important players in the intricate process of genetic regulation are the HOX genes. Many diseases, especially in the area of cancer, are linked to their aberrant functioning. Due to their distinctive functions in biomedical research-particularly in the complex process of tumor advancement-HOXA9 and HOXB9 have drawn particular attention. HOXA9 and HOXB9 are more significant than what is usually connected with HOX genes since they have roles in the intricate field of cancer and beyond embryonic processes. The framework for a focused study of the different effects of HOXA9 and HOXB9 in the context of tumor biology is established in this study.

Phenotypical innovations during evolution are caused by novel mutations, which are usually heterozygous at the beginning. The gene expressions on two alleles of these mutation sites are not necessarily identical, leading to flexible allele-specific regulation in cell systems. We retrieve the transcriptome data of normal and non-small cell lung cancer (NSCLC) tissues from 47 African Americans (AA) and 50 European Americans (EA). We analyze the differentially expressed genes (DEGs) in NSCLC as well as the tumor-specific mutations. Expression and mutation profiles show convergent evolution in AA and EA populations. The tumor-specific mutations are poorly overlapped, but many of them are located in the same genes, mainly oncogenes and tumor suppressor genes. The DEGs in tumors are majorly caused by the mutated alleles rather than normal alleles. The relative expressions of mutated alleles are highly correlated between AA and EA. The differential expression in NSCLC is predominantly mediated by the mutated alleles on heterozygous sites. This molecular mechanism underlying NSCLC oncogenesis is conserved across different human populations, exhibiting convergent evolution. We present this novel angle that differential expression analysis should be performed separately for different alleles. Our ideas should greatly benefit the cancer community.

Retinopathy of prematurity (ROP) is a major cause of childhood blindness worldwide, linked to gene variants in the renin-angiotensin-aldosterone system, including angiotensin-converting enzyme (ACE) and angiotensin II receptor type 1 (AGTR1). This study aims to evaluate the association between ACE insertion/deletion (I/D) and AGTR1 rs5186A > C variants with the occurrence and progression of ROP in a Polish cohort. A total of 377 premature infants were enrolled in the study. The ACE variant was evaluated using PCR, and AGTR1 was assessed using TaqMan probes. Clinical characteristics, including risk factors and comorbidities, were documented. A meta-analysis of the effects of the studied variants on ROP was also conducted. The AGTR1 rs5186C allele was significantly associated with both the progression of ROP and treatment outcomes. Homozygotes exhibited a 2.47-fold increased risk of developing proliferative ROP and a 4.82-fold increased risk of treatment failure. The impact of this allele increased at low birth weight. A meta-analysis, including 191 cases and 1661 controls, indicated an overall risk of 1.7 (95%CI 1.02-2.84) for the recessive effect of the rs5186C allele. The ACE variant did not show a significant association with ROP in our population; however, a meta-analysis of 996 cases and 2787 controls suggested a recessive effect of the insertion allele (an odds ratio of 1.21 (95%CI 1.00-1.60)). These results indicate that gain-of-function AGTR1 variants may play a crucial role in the development of ROP, potentially by promoting angiogenesis and pro-inflammatory effects. Screening for these variants could facilitate the development of personalized risk assessment and treatment strategies for ROP.

We report three patients with the novel variant c.100 + 1G > A of the TBCE gene and describe the presented clinical phenotype in detail. We also systematically reviewed the literature for clinical similarities and dissimilarities among all known patients with pathogenic TBCE variants. The clinical phenotype observed in patients with pathogenic TBCE variants is broader than previously described. Homozygous carriers of the c.100 + 1G > A variant exhibit a markedly milder clinical course, with no deviations in the calcium-phosphate metabolism and central nervous system pathology in MRI studies. Additionally, two patients manifest highly specific symptoms such as a rigid spine, eosinophilia, neutropenia, and nocturnal hypoxemia. Furthermore, cryptorchidism was observed in male patients. The identification of the pathogenic c.100 + 1G > A variant has thus far been limited to patients of Central-Eastern European descent, suggesting a potential founder mutation in this population.

Urofacial syndrome or Ochoa syndrome (UFS or UFOS) is a rare disease characterized by inverted facial expression and bladder dysfunction that was described for the first time in Colombia. It is an autosomal recessive pathology with mutations in the HPSE2 and LRIG2 genes. However, 16% of patients do not have any mutations associated with the syndrome. Despite the importance of neurobiology in its pathophysiology, there are no neurological, neuropsychological, or psychological studies in these patients. A 30-year-old male from Medellín, Colombia, with a significant perinatal history, was diagnosed with grade 4 hydronephrosis on his first ultrasound test. At 4 months of age, symptoms such as hypomimia, lagophthalmos, and recurrent urinary tract infections started to manifest. Imaging studies revealed urinary tract dilatation, vesicoureteral reflux, and a double collector system on his left side, which led to the diagnosis of UFS. Multiple procedures, including vesicostomy, ureterostomy, and enterocystoplasty, were performed. At 20 years of age, he achieved urinary sphincter control. Genetic analysis revealed a founder pathogenic variant, c.1516C > T (p.Arg506Ter), in the HPSE2 gene, which produces a truncated protein that lacks 86 amino acids. This variant is classified as pathogenic according to the ClinVar database for UFS. The mutation age is approximately 260-360 years, and the two alleles share a 7.2-7.4 Mb IBD segment. Moreover, we detected European local ancestry in the IBD segment, which is consistent with a Spanish introduction. Neurological examination, neuropsychological assessment, and psychological testing revealed no abnormalities, except for high stress levels. Clinical analysis of this patient revealed distorted facial expression and detrusor-sphincter dyssynergia, which are typical of patients with UFS. Genetic analysis revealed a pathogenic variant in the HPSE2 gene of European origin and a mutation age of 260-360 years. From a neurological, neuropsychological, and psychological (emotional and personality) perspective, the patient showed no signs or symptoms of clinical interest.

Chromosome 22q11.2 deletion syndrome (22q11.2DS) is a developmental disorder with high rates of anxiety and psychosis. Catechol-O-methyltransferase (COMT) regulates epinephrine (E), norepinephrine (NE), and dopamine (DA) and is implicated in both anxiety and psychotic disorders. The aim of this study was to determine how COMT variation relates to psychological anxiety and associated stress physiology responsiveness to better understand symptom heterogeneity in people with 22q11.2DS. We examined COMT allelic variation in relation to anxiety and hypothalamic-pituitary-adrenocortical (HPA) and sympathetic-adrenomedullary (SAM) hormonal stress indicators in 30 children and adolescents with 22q11.2DS. Contrary to expectation, individuals with the higher activity COMTval allele had higher anxiety levels versus those with the low activity (COMTmet) allele (p = 0.021; Glass' Δ = 0.69). Anxiety was not correlated with salivary cortisol (CORT) or alpha-amylase (sAA) in either group. Groups did not differ in CORT levels (p = 0.58), but the COMTmet group had higher sAA (p = 0.026; Glass' Δ = 0.67, uncorrected) suggesting greater SAM reactivity but not HPA activity. This suggests that COMT allelic variation may contribute to differences in acute SAM but not slower HPA stress reactivity in those with 22q11.2DS.

The present investigation was taken up to study the G × E interaction and stability in 14 sugarcane clones during 2020–2021 and 2021–2022 at four different locations namely Pantnagar, Kashipur, Dhanauri (Haridwar), and Dhakrani (Dehradun) for cane yield (CY) and sugar yield (SY) at the 10-month and 12-month stages. The research aimed to identify stable, high-yielding sugarcane clones adaptable to diverse environmental conditions, enhancing productivity and profitability for farmers in Uttarakhand, India. The combined ANOVA revealed significant differences among the clones (22.20% to 29.54% variation), environments (35% to 39.62% variation), and their interactions (19.91% to 24.16% variation) for CY and SY at both stages. To analyze the stability of genotypes and G × E interactions, the GGE biplot method was employed. The first two PCs explained 77.94% for CY, 74.39% for SY at the 10-month stage, and 81.01% for SY at 12-month stage of the total variation of the GGE model. The GGE biplots revealed that for CY, the mega-environment exhibited CoPant 16222 and CoPant 16223 as the winning genotypes. For SY at the 10-month stage, CoPant 17221 and CoPant 16222 were the best clones in two different mega-environments, while at the 12-month stage, the mega-environment showed CoPant 16222 and CoPant 16223 as the winning genotypes. Dehradun (2020) and Kashipur (2020) were identified as the best test environments for selecting widely and specifically adapted genotypes, respectively, for CY and SY at the 10-month as well as 12-month stages. In a nutshell, GGE biplot analysis identified the best-performing sugarcane clones and best test environments in Uttarakhand, India. Clone CoPant 16222 showed high mean performance and stability for cane and sugar yield, making it suitable for recommendation to farmers.

Acute myeloid leukemia (AML) is characterized by the uncontrolled proliferation of myeloid leukemia cells in the bone marrow and other hematopoietic tissues and is highly heterogeneous. While with the progress of sequencing technology, understanding of the AML-related biomarkers is still incomplete. The purpose of this study is to identify potential biomarkers for prognosis of AML. Based on WGCNA analysis of gene mutation expression, methylation level distribution, mRNA expression, and AML-related genes in public databases were employed for investigating potential biomarkers for the prognosis of AML. This study screened a total of 6153 genes by analyzing various changes in 103 acute myeloid leukemia (AML) samples, including gene mutation expression, methylation level distribution, mRNA expression, and AML-related genes in public databases. Moreover, seven AML-related co-expression modules were mined by WGCNA analysis, and twelve biomarkers associated with the AML prognosis were identified from each top 10 genes of the seven co-expression modules. The AML samples were then classified into two subgroups, the prognosis of which is significantly different, based on the expression of these twelve genes. The differentially expressed 7 genes of two subgroups (HOXB-AS3, HOXB3, SLC9C2, CPNE8, MEG8, S1PR5, MIR196B) are mainly involved in glucose metabolism, glutathione biosynthesis, small G protein-mediated signal transduction, and the Rap1 signaling pathway. With the utilization of WGCNA mining, seven gene co-expression modules were identified from the TCGA database, and there are unreported genes that may be potential driver genes of AML and may be the direction to identify the possible molecular signatures to predict survival of AML patients and help guide experiments for potential clinical drug targets.