ABSTRACT
Fetal hyperechogenic kidneys (HEK) is etiologically a heterogeneous disorder. The aim of this study was to identify the genetic causes of HEK using prenatal chromosomal microarray analysis (CMA) and exome sequencing (ES). From June 2014 to September 2022, we identified 92 HEK fetuses detected by ultrasound. We reviewed and documented other ultrasound anomalies, microscopic and submicroscopic chromosomal abnormalities, and single gene disorders. We also analyzed the diagnostic yield of CMA and ES and the clinical impact the diagnosis had on pregnancy management. In our cohort, CMA detected 27 pathogenic copy number variations (CNVs) in 25 (25/92, 27.2%) fetuses, with the most common CNV being 17q12 microdeletion syndrome. Among the 26 fetuses who underwent further ES testing, we identified 7 pathogenic/likely pathogenic variants and 8 variants of uncertain significance in 9 genes in 12 fetuses. Four novel variants were first reported herein, expanding the mutational spectra for HEK-related genes. Following counseling, 52 families chose to continue the pregnancy, and in 23 of them, postnatal ultrasound showed no detectable renal abnormalities. Of these 23 cases, 15 had isolated HEK on prenatal ultrasound. Taken together, our study showed a high rate of detectable genetic etiologies in cases with fetal HEK at the levels of chromosomal (aneuploidy), sub-chromosomal (microdeletions/microduplications), and single gene (point mutations). Therefore, we speculate that combined CMA and ES testing for fetal HEK is feasible and has good clinical utility. When no genetic abnormalities are identified, the findings can be transient, especially in the isolated HEK group.
Subject(s)
DNA Copy Number Variations , Prenatal Diagnosis , Pregnancy , Female , Humans , Exome Sequencing , Chromosome Aberrations , Fetus/diagnostic imaging , Fetus/abnormalities , Microarray Analysis , Kidney/diagnostic imagingABSTRACT
OBJECTIVE: To investigate the application value of whole exome sequencing technology in fetuses with congenital structural abnormalities. METHODS: The chromosomal abnormalities of 1147 families were analyzed. According to the follow-up results, the data of fetuses with new phenotypes in late pregnancy or after birth were reanalyzed. Subgroups were divided according to the organs involved and whether single malformation or not. The gene regulatory network map was drawn by using string database and Cytoscape software. Fisher exact probability method was used to compare the difference of the diagnostic rate of pathogenic genes among the groups. RESULTS: A total of 160 fetal cases received positive molecular diagnosed, involving 178 variant sites of 125 pathogenic genes, including 8 cases (4.9%, 8/163) by data reanalysis, and the overall positive diagnosis rate was 13.9%. Diagnostic rate was highest in the group of skeletal malformation (31.5%, 39/124) and lowest in that with thoracic malformation (0, 0/32). The gene clusters of fetal edema and intrauterine growth restriction were independent, and were not associated with the major structural malformations. The probability of each parent carrying the same recessive gene variant was 0.03 (39/1146) and 0.08 (4/53) with positive family history. CONCLUSION: For fetuses with congenital structural abnormalities that are negative for conventional genetic tests, 13.9% of phenotypic associated pathogenic/likely pathogenic genetic variants can be detected by whole exome sequencing technology. Its application value for prenatal diagnosis varies in fetus with different organs involved. Reanalysis of sequencing data for cases with new phenotypes in late pregnancy or after birth can further improve the molecular diagnosis rate. Further investigations are needed to explore the related genetic mechanisms.
Subject(s)
Fetal Diseases , Fetus , Female , Fetus/diagnostic imaging , Humans , Pregnancy , Prenatal Diagnosis , Technology , Ultrasonography, Prenatal , Exome SequencingABSTRACT
The pluripotent mouse embryonal carcinoma cell line P19 is widely used as a model for research on all-trans-retinoid acid (RA)-induced neuronal differentiation; however, the signaling pathways involved in this process remain unclear. This study aimed to reveal the molecular mechanism underlying the RA-induced neuronal differentiation of P19 cells. Real-time quantitative polymerase chain reaction and Western blot analysis were used to determine the expression of neuronal-specific markers, whereas flow cytometry was used to analyze cell cycle and cell apoptosis. The expression profiles of messenger RNAs (mRNAs) in RA-induced neuronal differentiation of P19 cells were analyzed using high-throughput sequencing, and the functions of differentially expressed mRNAs (DEMs) were determined by bioinformatics analysis. RA induced an increase in both class III ß-tubulin (TUBB3) and neurofilament medium (NEFM) mRNA expression, indicating that RA successfully induces neuronal differentiation of P19 cells. Cell apoptosis was not affected; however, cell proliferation decreased. We found 4117 DEMs, which were enriched in the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) signaling pathway, Wnt signaling pathway, and cell cycle. Particularly, a few DEMs could be identified in the PI3K/Akt signaling pathway networks, such as PI3K, Akt, glycogen synthase kinase-3ß (GSK3ß), cyclin-dependent kinase 4 (CDK4), P21, and Bax. RA significantly increased the protein expression of PI3K, Akt, phosphorylated Akt, GSK3ß, phosphorylated GSK3ß, CDK4, and P21, but it reduced Bax protein expression. The Akt inhibitor affected the increase of TUBB3 and NEFM mRNA expression in RA-induced P19 cells. The molecular mechanism underlying the RA-induced neuronal differentiation of P19 cells is potentially involved in the PI3K/Akt/GSK3ß signaling pathway. The decreased cell proliferation ability of neuronally differentiated P19 cells could be associated with the expression of cell cycle proteins.
Subject(s)
Carcinoma, Embryonal/pathology , Cell Differentiation , Glycogen Synthase Kinase 3 beta/metabolism , Neurons/pathology , Phosphatidylinositol 3-Kinases/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Tretinoin/pharmacology , Animals , Antineoplastic Agents/pharmacology , Apoptosis , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Carcinoma, Embryonal/drug therapy , Carcinoma, Embryonal/genetics , Carcinoma, Embryonal/metabolism , Cell Movement , Cell Proliferation , Gene Expression Regulation, Neoplastic , Glycogen Synthase Kinase 3 beta/genetics , Mice , Neurons/drug effects , Neurons/metabolism , Phosphatidylinositol 3-Kinases/genetics , Proto-Oncogene Proteins c-akt/genetics , Tumor Cells, CulturedABSTRACT
OBJECTIVE: We aimed to investigate the value of whole-exome sequencing (WES) in fetuses with congenital anomalies of the kidney and urinary tract (CAKUT) with or without other structural anomalies but with normal findings upon karyotyping and chromosome microarray analysis (CMA). METHODS: Cases with CAKUT with or without other structural anomalies were screened for eligibility. Fetuses with abnormal karyotyping or CMA results were excluded. We performed WES on DNA samples from eligible fetus-parental trios and identified diagnostic genetic variants based on ultrasonographic features. RESULTS: A total of 163 eligible fetus-parental trios were successfully analyzed by WES. We found 26 likely pathogenic or pathogenic variants in 18 genes from 20 fetuses, with a total proportion of diagnostic genetic variants of 12.3% (20/163). Genetic variants were significantly more frequently detected in fetuses with multisystem anomalies (27.0%, 10/37), enlarged kidney/echogenic kidney (20%, 4/20), and multicystic dysplastic kidney (11.1%, 4/36). Pregnancy outcome data showed that 88 (94.6%, 88/93) of the surviving cases with negative WES results had a good prognosis in early childhood. CONCLUSIONS: Our study is the largest to use WES prenatally for CAKUT and shows that WES can be used diagnostically to define the molecular defects that underlie unexplained CAKUT.
Subject(s)
Exome Sequencing , Kidney/abnormalities , Urinary Tract/abnormalities , Urogenital Abnormalities/diagnosis , Adolescent , Adult , China/epidemiology , Cohort Studies , Diagnosis, Differential , Female , Fetus/abnormalities , Fetus/diagnostic imaging , Genetic Testing/methods , Genetic Testing/statistics & numerical data , Humans , Kidney/diagnostic imaging , Male , Middle Aged , Predictive Value of Tests , Pregnancy , Prenatal Diagnosis/methods , Prenatal Diagnosis/statistics & numerical data , Ultrasonography, Prenatal , Urinary Tract/diagnostic imaging , Urogenital Abnormalities/epidemiology , Urogenital Abnormalities/genetics , Exome Sequencing/statistics & numerical data , Young AdultABSTRACT
OBJECTIVE: To assess the value of chromosome microarray analysis (CMA) and whole exome sequencing (WES) in fetuses with cerebellar vermis defects (CVD). METHODS: From 2013 to 2019, we performed CMA on 43 fetuses with CVD, who were divided into cerebellar vermis hypoplasia (CVH) group and Dandy-Walker malformation (DWM) group according to morphological subtypes. Subsequently, WES was performed on 19 fetuses with normal CMA results to identify diagnostic genetic variants (DGVs). RESULTS: Chromosome aneuploidies and clinically significant copy number variants were identified in 23.3% (10/43) of fetuses, and a significantly higher positive rate was found in fetuses with multiple compared with isolated malformations (36% vs 5.6%, P = .028). STAG2 genes related to Xq25 duplication syndrome was possibly a novel candidate gene for CVD. WES detected eight DGVs in seven genes among the 19 fetuses tested. Autosomal recessive ciliopathies (4/8) caused by TMEM231, CSPP1, and CEP290 mutations, were the most frequent monogenetic diseases, followed by Opitz GBBB syndrome (2/8) caused by MID1 and SPECC1L variants. CONCLUSION: The combined use of CMA and WES has the potential to provide genetic diagnoses in 42% (18/43) of fetal CVD. WES should be offered when CMA results are normal.
Subject(s)
Cerebellar Vermis/abnormalities , Genetic Counseling , Genetic Testing , Nervous System Malformations/diagnosis , Prenatal Diagnosis , Adult , Aneuploidy , Cerebellar Vermis/diagnostic imaging , China , Chromosome Aberrations/embryology , Female , Fetus/abnormalities , Fetus/diagnostic imaging , Genetic Counseling/methods , Genetic Testing/methods , Humans , Magnetic Resonance Imaging , Male , Microarray Analysis/methods , Nervous System Malformations/genetics , Pregnancy , Pregnancy Outcome , Prenatal Diagnosis/methods , Retrospective Studies , Ultrasonography, Prenatal , Exome Sequencing/methods , Young AdultSubject(s)
Fetal Growth Retardation , Pre-Eclampsia , Causality , Fetal Growth Retardation/genetics , HumansABSTRACT
OBJECTIVE: Duplex kidney is a relatively frequent form of urinary system abnormality. This study aimed to elucidate the value of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) for duplex kidney and the perinatal outcomes of duplex kidney fetuses. METHODS: This retrospective cohort study included 63 patients with duplex kidney diagnosed using antenatal ultrasound between August 2013 and January 2023. We reviewed the clinical characteristics, genetic test results, and pregnancy outcomes of the patients. RESULTS: Among the 63 cases based on the inclusion criteria, the CMA detected seven (11.1%) clinically significant variants and nine variants of uncertain significance (VUS), and the pathogenic/likely pathogenic (P/LP) copy number variations (CNVs) in the recurrent region that were associated with prenatal duplex kidney included 17q12, 17p13.3, and 22q11.2. No significant disparity was observed in the CMA detection rate between the unilateral and bilateral groups, or between the isolated and non-isolated groups. WES identified three (50%) P/LP single-gene variants in six fetuses with duplex kidney. We detected the following pathogenic genes in the duplex kidney fetuses: KMT2D, SMPD4, and FANCI. Pregnancy termination in cases where clinically significant variants were detected by genetic testing was different in statistical significance from that in cases with negative results (9/10, 90.0% vs 8/48, 16.7%, P < 0.001). CONCLUSION: This study elucidated the value of CMA and WES for fetal duplex kidney, proving that CMA and WES may be useful tools in prenatal diagnosis and genetic counseling.
Subject(s)
Exome Sequencing , Kidney , Ultrasonography, Prenatal , Humans , Female , Pregnancy , Retrospective Studies , Adult , Kidney/abnormalities , Kidney/diagnostic imaging , Pregnancy Outcome , Prenatal Diagnosis/methods , DNA Copy Number Variations , Urogenital Abnormalities/genetics , Urogenital Abnormalities/diagnostic imaging , Urogenital Abnormalities/diagnosis , Genetic Testing/methods , Microarray AnalysisABSTRACT
BACKGROUND: The molecular mechanism of fetal cystic hygroma (CH) is still unclear, and no study has previously reported the transcriptome changes of single cells in CH. In this study, single-cell transcriptome sequencing (scRNA-seq) was used to investigate the characteristics of cell subsets in the lesion tissues of CH patients. METHODS: Lymphoid tissue collected from CH patients and control donors for scRNA-seq analysis. Differentially expressed gene enrichment in major cell subpopulations as well as cell-cell communication were analyzed. At the same time, the expression and interactions of important VEGF signaling pathway molecules were analyzed, and potential transcription factors that could bind to KDR (VEGFR2) were predicted. RESULTS: The results of scRNA-seq showed that fibroblasts accounted for the largest proportion in the lymphatic lesions of CH patients. There was a significant increase in the proportion of lymphatic endothelial cell subsets between the cases and controls. The VEGF signaling pathway is enriched in lymphatic endothelial cells and participates in the regulation of cell-cell communication between lymphatic endothelial cells and other cells. The key regulatory gene KDR in the VEGF signaling pathway is highly expressed in CH patients and interacts with other differentially expressed EDN1, TAGLN, and CLDN5 Finally, we found that STAT1 could bind to the KDR promoter region, which may play an important role in promoting KDR up-regulation. CONCLUSION: Our comprehensive delineation of the cellular composition in tumor tissues of CH patients using single-cell RNA-sequencing identified the enrichment of lymphatic endothelial cells in CH and highlighted the activation of the VEGF signaling pathway in lymphoid endothelial cells as a potential modulator. The molecular and cellular pathogenesis of fetal cystic hygroma (CH) remains largely unknown. This study examined the distribution and gene expression signature of each cell subpopulation and the possible role of VEGF signaling in lymphatic endothelial cells in regulating the progression of CH by single-cell transcriptome sequencing. The enrichment of lymphatic endothelial cells in CH and the activation of the VEGF signaling pathway in lymphatic endothelial cells provide some clues to the pathogenesis of CH from the perspective of cell subpopulations.
Subject(s)
Lymphangioma, Cystic , Single-Cell Analysis , Vascular Endothelial Growth Factor Receptor-2 , Humans , Lymphangioma, Cystic/genetics , Lymphangioma, Cystic/metabolism , Lymphangioma, Cystic/pathology , Female , Vascular Endothelial Growth Factor Receptor-2/metabolism , Vascular Endothelial Growth Factor Receptor-2/genetics , Sequence Analysis, RNA , Signal Transduction , Vascular Endothelial Growth Factor A/metabolism , Vascular Endothelial Growth Factor A/genetics , STAT1 Transcription Factor/metabolism , STAT1 Transcription Factor/genetics , TranscriptomeABSTRACT
BACKGROUND: Brain development is an extremely complex and precisely regulated process, with about one-third of genes expressed and precisely regulated during brain development. OBJECTIVE: This study aims to explore the molecular mechanisms involved in brain development. METHODS: We first established the expression profile of long non-coding RNAs (lncRNAs) and mRNAs in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d through high-throughput sequencing. Second, the associated functions, pathways, and networks of the co-differentially expressed lncRNAs and mRNAs were identified via Gene Ontology (GO), pathway analysis, and PPI network. After bioinformatic analysis and screening, 8 differentially expressed lncRNAs and mRNAs with the same genetic origin were verified by RT-qPCR analysis in brain tissues of fetal mice at different developmental stages. RESULTS: The data revealed that there were 972 co-differentially expressed lncRNAs and 992 codifferentially expressed mRNAs in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d. And we discovered 125 differentially expressed lncRNAs and mRNAs, which have the same genetic origin, in brain tissues of fetal mice at 12.5d, 14.5d and 16.5d through sequencing results and bioinformatics analysis. Besides, we proved that 8 lncRNAs, which have had the same genetic origin as differentially expressed mRNAs, were prominently downregulated, while their maternal genes were upregulated during brain development in fetal mice. CONCLUSION: Our results preliminarily illustrated the differentially expressed lncRNAs and mRNAs, both of which were derived from the same parent genes, during brain development in fetal mice, which suggests that alternative splicing of lncRNA exists during brain development. Besides, our study provides a perspective on critical genes for brain development, which might be the underlying therapeutic targets for developmental brain diseases in children.
Subject(s)
Gene Expression Profiling , RNA, Long Noncoding , Mice , Animals , Gene Expression Profiling/methods , Oligonucleotide Array Sequence Analysis , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Alternative Splicing/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Brain/metabolismABSTRACT
PPP2R1A-related neurodevelopmental disorder (NDD) is expressed with autosomal dominant inheritance and is typically caused by a pathogenic de novo PPP2R1A mutation. It is characterized by the predominant features of hypotonia, developmental delay, moderate-to-severe intellectual disability, agenesis of corpus callosum (ACC), ventriculomegaly, and dysmorphic features; however, none of these anomalies have been diagnosed prenatally. We report on the prenatal diagnosis of PPP2R1A-related NDD in two fetuses by whole exome sequencing. Fetus 1 had partial ACC and severe lateral ventriculomegaly; the pathogenic heterozygous c.544C > T (p. Arg182Trp) de novo missense variant in PPP2R1A was detected. Fetus 2 had severe enlargement of the lateral and third ventricles and macrocephaly; they showed a heterozygous likely pathogenic mutation in PPP2R1A gene (c.547C > T, p. Arg183Trp). Both variants were de novo. This was the first study to use trio WES to prenatally analyze fetuses with PPP2R1A variants. Prenatal diagnosis will not only expand the fetal phenotype of this rare genetic condition but also allow for an appropriate counseling of prospective parents regarding pregnancy outcomes.
Subject(s)
Hydrocephalus , Nervous System Malformations , Neurodevelopmental Disorders , Pregnancy , Female , Humans , Exome Sequencing , Prospective Studies , Prenatal Diagnosis , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/genetics , Transcription Factors , Protein Phosphatase 2/geneticsABSTRACT
Congenital heart disease (CHD) is a serious condition with unknown etiology. In a recent study, a compound heterozygous mutation (c.3526C > T [p.Arg1176Trp] and c.4643A > G [p.Asp1548Gly]) in the ASXL3 gene was identified, which is associated with CHD. This mutation was overexpressed in HL-1 mouse cardiomyocyte cells, leading to increased cell apoptosis and decreased cell proliferation. However, whether this effect is mediated by long noncoding RNAs (lncRNAs) is yet to be determined. We identified the differences among lncRNA and mRNA profiles in mouse heart tissues using sequencing to explore this issue. We detected HL-1 cell proliferation and apoptosis through CCK8 and flow cytometry. Fgfr2, lncRNA, and Ras/ERK signaling pathway expressions were evaluated using quantitative real time polymerase chain reaction (qRT-PCR) and western blot (WB) assays. We also conducted functional investigations by silencing lncRNA NONMMUT063967.2. The sequencing revealed significant changes in lncRNA and mRNA profiles, with the expression of lncRNA NONMMUT063967.2 being significantly promoted in the ASXL3 gene mutations group (MT) while the expression of Fgfr2 being downregulated. The in vitro experiments showed that ASXL3 gene mutations inhibited the proliferation of cardiomyocytes and accelerated cell apoptosis by promoting the expression of lncRNAs (NONMMUT063967.2, NONMMUT063918.2, and NONMMUT063891.2), suppressing the formation of FGFR2 transcripts, and inhibiting the Ras/ERK signaling pathway. The decrease in FGFR2 had the same effect on the Ras/ERK signaling pathway, proliferation, and apoptosis in mouse cardiomyocytes as ASXL3 mutations. Further mechanistic studies revealed that suppression of lncRNA NONMMUT063967.2 and overexpression of FGFR2 reversed the effects of the ASXL3 mutations on the Ras/ERK signaling pathway, proliferation, and apoptosis in mouse cardiomyocytes. Therefore, ASXL3 mutation decreases FGFR2 expression by upregulating lncRNA NONMMUT063967.2, inhibiting cell proliferation and promoting cell apoptosis in mouse cardiomyocytes.
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OBJECTIVE: SHOX haploinsufficiency have been commonly found in isolated short stature (ISS) and Léri-Weill dyschondrosteosis (LWD) patients. However, few publications have described the genetic analysis and clinical characteristics of fetuses with SHOX haploinsufficiency. METHODS: Chromosomal microarray (CMA) were applied in 14,051 fetuses and sequentially whole exome sequence (WES) in 1340 fetuses who underwent prenatal diagnosis during 2016-2021. The analysis and summary of molecular genetics, sonographic characteristics, and follow-up results were performed in fetuses with SHOX haploinsufficiency without other genetic etiologies. A comparison was made between three groups according to prenatal diagnostic indications. RESULTS: 8 (0.06%) fetuses of SHOX haploinsufficiency were all detected by CMA, of which 5 (62.5%) were detected with short long bones by ultrasound scan, and 4 were inherited from their previously undiagnosed parents. No pathogenic SHOX variants were found by WES. The detection rate of SHOX haploinsufficiency was obviously higher in the short long bone group (2.6%, 5/191) than the other abnormality group (0.03%, 1/3919) or no ultrasound abnormality group (0.02%, 2/9941). Three of the fetuses were liveborn with normal growth up to the age of four and four were terminated. CONCLUSION: The phenotype of fetuses with SHOX haploinsufficiency is highly varied. Over 1/3 of the cases exhibited no phenotype and nearly 2/3 with short long bones, in the absence of Madelung deformity during fetal development. SHOX haploinsufficiency should be considered in all antenatal presentations, especially in the case of isolated short long bones. CMA can provide effective detection.
Subject(s)
Haploinsufficiency , Homeodomain Proteins , Female , Pregnancy , Humans , Homeodomain Proteins/genetics , Short Stature Homeobox Protein/genetics , Haploinsufficiency/genetics , Growth Disorders/genetics , Fetus/diagnostic imagingABSTRACT
Background: Microcephaly is common in patients with neuropsychiatric problems, and it is usually closely related to genetic causes. However, studies on chromosomal abnormalities and single-gene disorders associated with fetal microcephaly are limited. Objective: We investigated the cytogenetic and monogenic risks of fetal microcephaly and evaluated their pregnancy outcomes. Methods: We performed a clinical evaluation, high-resolution chromosomal microarray analysis (CMA), and trio exome sequencing (ES) on 224 fetuses with prenatal microcephaly and closely followed the pregnancy outcome and prognosis. Results: Among 224 cases of prenatal fetal microcephaly, the diagnosis rate was 3.74% (7/187) for CMA and 19.14% (31/162) for trio-ES. Exome sequencing identified 31 pathogenic or likely pathogenic (P/LP) single nucleotide variants (SNVs) in 25 genes associated with fetal structural abnormalities in 37 microcephaly fetuses; 19 (61.29%) of which occurred de novo. Variants of unknown significance (VUS) was found in 33/162 (20.3%) fetuses. The gene variant involved included the single gene MPCH 2 and MPCH 11, which is associated with human microcephaly, and HDAC8, TUBGCP6, NIPBL, FANCI, PDHA1, UBE3A, CASK, TUBB2A, PEX1, PPFIBP1, KNL1, SLC26A4, SKIV2L, COL1A2, EBP, ANKRD11, MYO18B, OSGEP, ZEB2, TRIO, CLCN5, CASK, and LAGE3. The live birth rate of fetal microcephaly in the syndromic microcephaly group was significantly higher than that in the primary microcephaly group [62.9% (117/186) vs 31.56% (12/38), p = 0.000]. Conclusion: We conducted a prenatal study by conducting CMA and ES for the genetic analysis of fetal microcephaly cases. CMA and ES had a high diagnostic rate for the genetic causes of fetal microcephaly cases. In this study, we also identified 14 novel variants, which expanded the disease spectrum of microcephaly-related genes.
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The Dandy-Walker malformation (DWM) is characterized by neuron dysregulation in embryonic development; however, the regulatory mechanisms associated with it are unclear. This study aimed to investigate the role of NADH dehydrogenase 1 alpha subcomplex 4 (NDUFA4) in regulating downstream signaling cascades and neuronal proliferation and apoptosis. Ndufa4 overexpression promoted the proliferation of neurons and inhibited their apoptosis in vitro, which underwent reverse regulation by the Ndufa4 short hairpin RNAs. Ndufa4-knockout (KO) mice showed abnormal histological alterations in the brain tissue, in addition to impaired spatial learning capacity and exploratory activity. Ndufa4 depletion altered the microRNA expressional profiles of the cerebellum: Ndufa4 inhibited miR-145a-5p expression both in the cerebellum and neurons. miR-145a-5p inhibited the proliferation of neurons and promoted their apoptosis. Ndufa4 promoted and miR-145a-5p inhibited the expression of human homer protein homolog 1 and cyclin D2 in neurons. Thus, Ndufa4 promotes the proliferation of neurons and inhibits their apoptosis by inhibiting miR-145a-5p, which directly targets and inhibits the untranslated regions of Homer1 and Ccnd2 expression.
Subject(s)
MicroRNAs , Mice , Animals , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Cyclin D2/metabolism , Apoptosis/genetics , Neurons/metabolism , Cell Proliferation/genetics , Electron Transport Complex IV/metabolism , Homer Scaffolding Proteins/metabolismABSTRACT
Soil water repellency (SWR) is a physical phenomenon whereby water cannot penetrate or has difficulty penetrating the soil surface. There are many factors involved in its occurrence, but the main factors controlling its emergence in loess remain unclear. In this work, we have studied numerous physicochemical and biological factors functioning in different dominant vegetations (Pinus tabulaeformis Carr., Robinia pseudoacacia L., and Hippophae rhamnoides L.) in a loess hilly region by gas chromatography-mass spectrometry (GC-MS) and high-throughput sequencing techniques. We observed that more than 75% of the soils under Robinia and Hippophae are categorized as slightly or strongly water repellent, while nearly 50% of the soils under Pinus are categorized as severely to extremely water repellent. The relative concentrations of total free lipids in the soil in the same water-repellency class were Pinus > Robinia > Hippophae, where fatty acids, alkanols, and sterols were positively correlated with SWR, whereas alkanes were not. For the abundance and diversity index of bacterial and fungal communities, the three species ranked in the following order: Robinia ≈ Hippophae > Pinus. Thus, solvent-extractable polar waxes were indicated to be better preserved in water-repellent soils under Pinus due to lower microbial diversity than Robinia and Hippophae. Here, we demonstrate polar waxes to be the principal factor controlling SWR. Moreover, the dominant phyla of fungi varied greatly than those of bacteria under three vegetation types. Correlation analysis showed that the abundance of Actinobacteria in dominant bacteria increased with SWR. Nonmetric multidimensional scaling suggested the fungal community in different water-repellent soils under Pinus to vary more than those under Robinia and Hippophae. The indicator species mainly belonged to Actinobacteria in bacteria and Basidiomycota in fungi at the phylum level; this finding was further supported by the linear discriminant analysis (LDA) effect size (LEfSe). Additionally, GC-MS identified a small amount of ergosterol, a specific biomarker of fungi under Pinus. These pieces of evidence collectively reveal that severe to extreme SWR occurs under Pinus and appears to be the most influenced by fungi and actinomycetes when the topsoil is close to air drying. However, there is a need for further testing on different plant species or land use.
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MYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth, biological and abiotic stress. Recent studies have revealed that some MYCs are involved in the synthesis of sulfur-containing secondary metabolites. Cabbage, as a typical sulfur-loving crop and rich in sulfur-containing secondary metabolites, the regulatory relationship between sulfur stress and MYC gene family, related reports are relatively rare. In this study, we conducted the first genome-wide analysis of the MYC transcription factor family of cabbage and identified 17 BoMYC genes. Homology of the 17 BoMYC genes, 12 Arabidopsis, 12 Chinese cabbage, 8 wheat and 21 maize MYC were analyzed using the phylogenetic analysis. Meanwhile, chromosome locations, physical and chemical characteristics, gene structures, conserved motif, cis-element, specific expression in different tissues were studied. Finally, we analyzed the expression of the BoMYC gene under sulfur stress and its GO annotation and KEGG enrichment analysis, determined the expression of the BoMYC gene under hormone treatment and the growth index, photosynthetic capacity and hormone content in the leaves. This study is of great significance for functional identification and revealed the effect of S on BoMYC transcription factors.
Subject(s)
Brassica/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Sulfur/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Amino Acid Motifs , Brassica/growth & development , Brassica/metabolism , Chromosome Mapping , Chromosomes, Plant , Conserved Sequence , Genes, Plant , Genome, Plant , Multigene Family , Photosynthesis , Plant Growth Regulators/metabolism , Promoter Regions, Genetic , Stress, PhysiologicalABSTRACT
Cruciferous vegetable crops are grown widely around the world, which supply a multitude of health-related micronutrients, phytochemicals, and antioxidant compounds. Glucosinolates (GSLs) are specialized metabolites found widely in cruciferous vegetables, which are not only related to flavor formation but also have anti-cancer, disease-resistance, and insect-resistance properties. The content and components of GSLs in the Cruciferae are not only related to genotypes and environmental factors but also are influenced by hormones, plant growth regulators, and mineral elements. This review discusses the effects of different exogenous substances on the GSL content and composition, and analyzes the molecular mechanism by which these substances regulate the biosynthesis of GSLs. Based on the current research status, future research directions are also proposed.
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Congenital heart disease (CHD) is the most common birth defect. Although ASXL transcriptional regulator 3 (ASXL3) has been reported to cause hereditary CHD, ASXL3-mediated mechanisms in heart development remain unclear. In this study, we used dimethyl sulfoxide (DMSO) to induce differentiation in P19 cells, observed cell morphology using light microscopy after ASXL3 knockdown, and determined the levels of associated myocardial cell markers using reverse transcription-quantitative polymerase chain reaction and western blotting. Subsequently, we used microRNA sequencing, messenger RNA (mRNA) sequencing, and bioinformatics to initially identify the possible mechanisms through which ASXL3-related microRNAs and mRNAs affect heart development. The results indicated that DMSO induced P19 cell differentiation, which could be inhibited by ASXL3 knockdown. We screened 1214 and 1652 differentially expressed microRNAs and mRNAs, respectively, through ASXL3 knockdown and sequencing; these differentially expressed miRNAs were largely enriched in PI3K-Akt, mitogen-activated protein kinase, and Rap1 signaling pathways. Additionally, 11 miRNAs associated with heart development were selected through a literature review. Our analysis indicated the involvement of mmu-miR-323-3p in P19 cell differentiation through the PI3K-Akt pathway. In conclusion, ASXL3 may be involved in the regulation of heart development. This comprehensive study of differentially expressed microRNAs and mRNAs through ASXL3 knockdown in P19 cells provides new insights that may aid the prevention and treatment of CHD.
Subject(s)
MicroRNAs , Dimethyl Sulfoxide , MicroRNAs/genetics , MicroRNAs/metabolism , Phosphatidylinositol 3-Kinases , Proto-Oncogene Proteins c-akt , RNA, Messenger/genetics , RNA, Messenger/metabolismABSTRACT
BACKGROUND: There are a few literature reports of prenatal ultrasound manifestations of Williams-Beuren syndrome. We aimed to explore the prenatal diagnosis of Williams-Beuren syndrome by ultrasound and chromosomal microarray analysis and describe the prenatal ultrasound performance of this syndrome. METHODS: In this retrospective study, we reported eight cases of Williams-Beuren syndrome diagnosed at our prenatal diagnostic center from 2016 to 2021. We systematically reviewed clinical data from these cases, including indications for invasive testing, sonographic findings, QF-PCR results, chromosomal microarray analysis results, and pregnancy outcomes. RESULTS: In this study, the common ultrasound features were ventricular septal defect (37.5%), intrauterine growth retardation (25%), and aortic coarctation (25%). Moreover, all patients were found to have a common deletion in the Williams-Beuren syndrome chromosome region at the 7q11.23 locus, which contained the elastin gene. Deletion sizes ranged from 1.42 to 2.07 Mb. Seven parents asked for termination of pregnancy, and one patient was lost to follow-up. CONCLUSIONS: This study is the most extensive prenatal study using chromosomal microarray analysis technology for detailed molecular analysis of Williams-Beuren syndrome cases. We reported three cases combined with first-reported ultrasound manifestations. Case 1 was concomitant with multicystic dysplastic kidney and duodenal atresia combined with case 3. Notably, case 4 was combined with multiple cardiovascular malformations: Tetralogy of Fallot, right aortic arch, and supravalvar aortic stenosis. These manifestations expand the intrauterine ultrasound phenotype of Williams-Beuren syndrome in previous literature reports.
ABSTRACT
BACKGROUND: Exome sequencing (ES) is becoming more widely available in prenatal diagnosis. However, data on its clinical utility and integration into clinical management remain limited in practice. Herein, we report our experience implementing prenatal ES (pES) in a large cohort of fetuses with anomalies detected by ultrasonography using a hospital-based in-house multidisciplinary team (MDT) facilitated by a three-step genotype-driven followed by phenotype-driven analysis framework. METHODS: We performed pES in 1618 fetal cases with positive ultrasound findings but negative for karyotyping and chromosome microarray analysis between January 2014 and October 2021, including both retrospective (n=565) and prospective (n=1053) cohorts. The diagnostic efficiency and its correlation to organ systems involved, phenotypic spectrum, and the clinical impacts of pES results on pregnancy outcomes were analyzed. RESULTS: A genotype-driven followed by phenotype-driven three-step approach was carried out in all trio pES. Step 1, a genotype-driven analysis resulted in a diagnostic rate of 11.6% (187/1618). Step 2, a phenotype-driven comprehensive analysis yielded additional diagnostic findings for another 28 cases (1.7%; 28/1618). In the final step 3, data reanalyses based on new phenotypes and/or clinical requests found molecular diagnosis in 14 additional cases (0.9%; 14/1618). Altogether, 229 fetal cases (14.2%) received a molecular diagnosis, with a higher positive rate in the retrospective than the prospective cohort (17.3% vs. 12.4%, p<0.01). The diagnostic rates were highest in fetuses with skeletal anomalies (30.4%) and multiple organ involvements (25.9%), and lowest in fetuses with chest anomalies (0%). In addition, incidental and secondary findings with childhood-onset disorders were detected in 11 (0.7%) cases. Furthermore, we described the prenatal phenotypes for the first time for 27 gene-associated conditions (20.0%, 27/135) upon a systematic analysis of the diagnosed cases and expanded the phenotype spectrum for 26 (19.3%) genes where limited fetal phenotypic information was available. In the prospective cohort, the combined prenatal ultrasound and pES results had significantly impacted the clinical decisions (61.5%, 648/1053). CONCLUSIONS: The genotype-driven approach could identify about 81.7% positive cases (11.6% of the total cohort) with the initial limited fetal phenotype information considered. The following two steps of phenotype-driven analysis and data reanalyses helped us find the causative variants in an additional 2.6% of the entire cohort (18.3% of all positive findings). Our extensive phenotype analysis on a large number of molecularly confirmed prenatal cases had greatly enriched our current knowledge on fetal phenotype-genotype correlation, which may guide more focused prenatal ultrasound in the future. This is by far the largest pES cohort study that combines a robust trio sequence data analysis, systematic phenotype-genotype correlation, and well-established MDT in a single prenatal clinical setting. This work underlines the value of pES as an essential component in prenatal diagnosis in guiding medical management and parental decision making.