T-box transcription factor T(TBXT;T)is required for mesodermal formation and axial skeletal development.Although it has been extensively studied in various model organisms,human congenital vertebral malformations(CVMs...T-box transcription factor T(TBXT;T)is required for mesodermal formation and axial skeletal development.Although it has been extensively studied in various model organisms,human congenital vertebral malformations(CVMs)involving T are not well established.Here,we report a family with 15 CVM patients distributed across 4 generations.All affected individuals carry a heterozygous mutation,T c.596A>G(p.Q199R),which is not found in unaffected family members,indicating co-segregation of the genotype and phenotype.In vitro assays show that T p.Q199R increases the nucleocytoplasmic ratio and enhances its DNA-binding affinity,but reduces its transcriptional activity compared to the wild-type.To determine the pathogenicity of this mutation in vivo,we generated a Q199R knock-in mouse model that recapitulates the human CVM phenotype.Most heterozygous Q199R mice show subtle kinked or shortened tails,while homozygous mice exhibit tail filaments and severe vertebral deformities.Overall,we show that the Q199R mutation in T causes CVM in humans and mice,providing previously unreported evidence supporting the function of T in the genetic etiology of human CVM.展开更多
INTRODUCTION Organoids are primary tissue or stem cells derived cell aggregates that have the capacity for self-organization,self-renewal,and the capacity to mimic cellular and tissue level functions.Organoids can ove...INTRODUCTION Organoids are primary tissue or stem cells derived cell aggregates that have the capacity for self-organization,self-renewal,and the capacity to mimic cellular and tissue level functions.Organoids can overcome the shortcomings of traditional 2D cell culture models and closely mimic 3D primary tissue composition.展开更多
Background： Marker detection is an important task in complex disease studies. Here we provide an association rule mining （ARM） based approach for identifying integrated markers through mutual information （MI） bas...Background： Marker detection is an important task in complex disease studies. Here we provide an association rule mining （ARM） based approach for identifying integrated markers through mutual information （MI） based statistically significant feature extraction, and apply it to acute myeloid leukemia （AML） and prostate carcinoma （PC） gene expression and methylation profiles. Methods： We first collect the genes having both expression and methylation values in AML as well as PC. Next, we run Jarque-Bera normality test on the expression/methylation data to divide the whole dataset into two parts： one that follows normal distribution and the other that does not follow normal distribution. Thus, we have now four parts of the dataset： normally distributed expression data, normally distributed methylation data, non-normally distributed expression data, and non-normally distributed methylated data. A feature-extraction technique, ＂mRMR＂ is then utilized on each part. This results in a list of top-ranked genes. Next, we apply Welch t-test （parametric test） and Shrink t-test （non-parametric test） on the expression/methylation data for the top selected normally distributed genes and non-normally distributed genes, respectively. We then use a recent weighted ARM method, ＂RANWAR＂ to combine all/specific resultant genes to generate top oncogenic rules along with respective integrated markers. Finally, we perform literature search as well as KEGG pathway and Gene-Ontology （GO） analyses using Enrichr database for in silico validation of the prioritized oncogenes as the markers and labeling the markers as existing or novel. Results： The novel markers of AML are {ABCB11↑ U KRT17↓} （i.e., ABCBll as up-regulated, ＆ KRT17 as down- regulated）, and {AP1SI-UKRT17↓ U NEIL2-UDYDC1↓}） （i.e., AP1S1 and NEIL2 both as hypo-methylated, ＆ KRT17 and DYDC1 both as down-regulated）. The novel marker of PC is {UBIAD1 ｜｜U APBA2 U C4orf31： （i.e., UBIAD1 as up-regulated and hypo-methylated, ＆ APBA2 and C4orf31 both as down-regulated and hyper- methylated）. Conclusion： The identified novel markers might have critical roles in AML as well as PC. The approach can be applied to other complex disease.展开更多
Identification of B-cell epitopes(BCEs)plays an essential role in the development of peptide vaccines and immuno-diagnostic reagents,as well as antibody design and production.In this work,we generated a large benchmar...Identification of B-cell epitopes(BCEs)plays an essential role in the development of peptide vaccines and immuno-diagnostic reagents,as well as antibody design and production.In this work,we generated a large benchmark dataset comprising 124,879 experimentally supported linear epitope-containing regions in 3567 protein clusters from over 1.3 million B cell assays.Analysis of this curated dataset showed large pathogen diversity covering 176 different families.The accuracy in linear BCE prediction was found to strongly vary with different features,while all sequencederived and structural features were informative.To search more efficient and interpretive feature representations,a ten-layer deep learning framework for linear BCE prediction,namely Net BCE,was developed.Net BCE achieved high accuracy and robust performance with the average area under the curve(AUC)value of 0.8455 in five-fold cross-validation through automatically learning the informative classification features.Net BCE substantially outperformed the conventional machine learning algorithms and other tools,with more than 22.06%improvement of AUC value compared to other tools using an independent dataset.Through investigating the output of important network modules in Net BCE,epitopes and non-epitopes tended to be presented in distinct regions with efficient feature representation along the network layer hierarchy.The Net BCE is freely available at https://github.com/bsml320/Net BCE.展开更多
Single-cell RNA sequencing(scRNA-seq)is revolutionizing the study of complex and dynamic cellular mechanisms.However,cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual ...Single-cell RNA sequencing(scRNA-seq)is revolutionizing the study of complex and dynamic cellular mechanisms.However,cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation,which is cumbersome and subjective.The increasing number of scRNA-seq datasets,as well as numerous published genetic studies,has motivated us to build a comprehensive human cell type reference atlas.Here,we present decoding Cell type Specificity(deCS),an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker genes.We used deCS to annotate scRNAseq data from various tissue types and systematically evaluated the annotation accuracy under different conditions,including reference panels,sequencing depth,and feature selection strategies.Our results demonstrate that expanding the references is critical for improving annotation accuracy.Compared to many existing state-of-the-art annotation tools,deCS significantly reduced computation time and increased accuracy.deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation.Finally,we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits,providing deep insights into the cellular mechanisms underlying disease pathogenesis.展开更多
Dear Colleagues,As an Executive Editor-in-Chief,I have edited this Special Issue(SI),entitled “Birth Defects:Issues and Advances in 2022”in the journal Reproductive and Developmental Medicine(RDM,ISSN:2096-2924,CN:1...Dear Colleagues,As an Executive Editor-in-Chief,I have edited this Special Issue(SI),entitled “Birth Defects:Issues and Advances in 2022”in the journal Reproductive and Developmental Medicine(RDM,ISSN:2096-2924,CN:10-1442/R),the first ever English journal in the field of reproductive medicine and developmental biology in China's Mainland.Since its launch in 2017,RDM has been dedicated to providing a good platform for academic exchanges among scientists,both at home and abroad.展开更多
Cleft lip with/without cleft palate(CL/P) is one of the most common congenital human birth defects with a prevalence estimated at approximately 1/700 live births worldwide, varying with gender,ethnicity, and geographi...Cleft lip with/without cleft palate(CL/P) is one of the most common congenital human birth defects with a prevalence estimated at approximately 1/700 live births worldwide, varying with gender,ethnicity, and geographic location[1]. Significant efforts have been made to understand CL/P pathogenesis.展开更多
Autosomal recessive spinocerebellar ataxias(SCARs)are one of the most common neurodegenerative diseases characterized by progressive ataxia.Although SCARs are known to be caused by mutations in multiple genes,there ar...Autosomal recessive spinocerebellar ataxias(SCARs)are one of the most common neurodegenerative diseases characterized by progressive ataxia.Although SCARs are known to be caused by mutations in multiple genes,there are still many cases that go undiagnosed or are misdiagnosed.In this study,we presented a SCAR patient,and identified a probable novel pathogenic mutation(c.1A>G,p.M1V)in the AFG3L2 start codon.The proband's genotype included heterozygous mutations of the compound AFG3L2(p.[M1V];[R632X](c.[1A>G];[1894.C>T])),which were inherited from the father(c.1A>G,p.M1V)and mother(c.1894C>T,p.R632X).Functional studies performed on hi PSCs(human induced pluripotent stem cells)generated from the patients and HEK293T cells showed that the mutations impair mitochondrial function and the unbalanced expression of AFG3L2 mRNA and protein levels.Furthermore,this novel mutation resulted in the degradation of the protein and the reduction of the stability of the AFG3L2 protein,and MCU(mitochondrial calcium uniporter)complex mediated Ca2+overload.展开更多
The challenges and breakthroughs in human genetics can largely depend on the depth of exploring the missing heritability[1]and understanding of genetic variants,which enabled scientists to better elucidate the underly...The challenges and breakthroughs in human genetics can largely depend on the depth of exploring the missing heritability[1]and understanding of genetic variants,which enabled scientists to better elucidate the underlying causes of diseases and apply this knowledge in clinical settings.Human genomes differ from one individual to another in the form of single nucleotide variants(SNVs),small insertions and deletions(indels)(<50 base pairs(bp)),and structural variants(SVs)[2].展开更多
Objective::To investigate the roles of transcription factors (TFs) in the etiology of complex human birth defects, including neural tube defects (NTDs), congenital heart diseases (CHDs), and hypospadias.Methods::We ex...Objective::To investigate the roles of transcription factors (TFs) in the etiology of complex human birth defects, including neural tube defects (NTDs), congenital heart diseases (CHDs), and hypospadias.Methods::We examined the overlap of genetically associated genes among NTDs, CHDs, and hypospadias. We then compared the expression profiles of these diseases based on all the detected genes and disease-associated TFs. The differentially expressed TFs that we obtained were further subjected to functional enrichment analysis to elucidate their role in the development of these birth defects.Results::TF genes were significantly enriched in complex birth defects ( P= 5.95 × 10^(-24)). NTDs, CHDs, and hypospadias showed distinct gene expression profiles compared with the controls. Although TFs could not efficiently separate CHDs from normal subjects, distinct gene expression profiles of TFs could distinguish NTDs and hypospadias from controls. Differentially expressed TFs can be used to characterize NTDs, hypospadias, and controls. The enriched TFs in biological processes (BPs) reflected the different morphological processes of NTDs, CHDs, and hypospadias. Conclusions::This study indicates that abnormal expression patterns of specific TFs may disrupt the normal requirements for developmental equilibrium through the related BPs. The investigation of genetically associated genes and gene expression profiles for the three different complex birth defects provides new insights into how the dysregulation of TFs influences their developmental process.展开更多
Objectives:Folates are B vitamins that are essential for several molecular,cellular,and biological processes,including nucleotide synthesis,methylation,and methionine cycling.The physiological impacts of these process...Objectives:Folates are B vitamins that are essential for several molecular,cellular,and biological processes,including nucleotide synthesis,methylation,and methionine cycling.The physiological impacts of these processes on health also extend to cell proliferation,folate deficiency anemia,and reduction of the risk of birth defects during pregnancy.The primary objective of this study was to characterize the binding affinities of different folate forms,folic acid(FA),5-methyltetrahydrofolate(5MTHF),and folinic acid,to the folate receptorsαandβ,and to the bovine milk folate binding protein.These three dietary forms of folate are found in enriched grains(FA),various fruits and leafy vegetables(folinic acid),and red blood cells(5MTHF).Methods:The half maximal inhibitory concentration values and binding curves of each of these folates for each receptor were determined.Results:Our results indicated that FA had the highest affinity for all folate receptors,followed by 5MTHF,and lastly,by folinic acid,examined by several orders of magnitudes.Conclusion:These data are expected to provide new insights into the therapeutic applications of the different forms of folate in a variety of diseases.展开更多
Objective::The prevalence of midline birth defects, such as gastroschisis, has increased worldwide, over the last few decades. This study aims to explore the prevalence, maternal epidemiological characteristics, and n...Objective::The prevalence of midline birth defects, such as gastroschisis, has increased worldwide, over the last few decades. This study aims to explore the prevalence, maternal epidemiological characteristics, and natural history of neonates affected by gastroschisis at the University Hospital of Leon city, Nicaragua.Methods:Data were collected from the birth defect surveillance system of the Hospital Oscar Danilo Rosales (HEODRA). The analysis included all pregnancies that had gastroschisis complications between January 1 and December 31, 2020. The prevalence of gastroschisis was calculated according to maternal age. The mothers were interviewed, and the clinical records of the newborns were reviewed.Results::Among the 4,460 deliveries included in this study, four cases of gastroschisis were identified, including three live births and one stillbirth. The gastroschisis rate was 8.9 per 10,000 live births (95% confidence interval [CI]: 0.18-17.8). The prevalence among mothers younger than 20 years and those older than 20 years was 26.4 (95% CI: -3.43 to 56.25) and 3.01 (95% CI: 2.89-8.90)/10,000 births, respectively. Mothers of gastroschisis-affected fetuses were of rural origin ( n = 3), had normal body mass indexes ( n = 3), were exposed to tobacco and wood smoke ( n = 2), and one was exposed to pesticides during the periconceptional period. Primary closure of the gastroschisis was performed on one patient, and complex gastroschisis for intestinal perforation was observed in another patient. The mean hospitalization duration was 33 days, and two patients were discharged alive. Conclusions::Gastroschisis was a significant birth defect among children delivered at HEODRA in 2020. Its prevalence in Nicaragua was higher than that in other countries in the region. All complicated pregnancies were young women with unplanned pregnancies, from rural areas, with exposure to secondhand smoke, and without vitamin supplements before or during the first trimester of pregnancy. Only 67% of infants survived after hospital discharge.展开更多
Objective:The purpose of this study was to examine the role of rare variants in the one-carbon metabolic pathway in the etiology of the cerebral folate deficiency(CFD)syndrome.The CFD syndrome is a neurometabolic synd...Objective:The purpose of this study was to examine the role of rare variants in the one-carbon metabolic pathway in the etiology of the cerebral folate deficiency(CFD)syndrome.The CFD syndrome is a neurometabolic syndrome identified by low concentrations of 5-methyltetrahydrofolate(5-MTHF)in the cerebrospinal fluid(CSF)in spite of near-normal peripheral folate levels resulting in neurodevelopmental disorders.Methods:The localized folate metabolism impairments in CFD are thought to be either the result of mutations in genes responsible for folate transport or folate turnover through degradation.Genes that have been previously implicated in the etiology of CFD include folate receptor alpha-1(FOLR1),dihydrofolate reductase,proton-coupled folate transporter,and capicua.We performed whole-exome sequencing(WES)analysis of a CFD patient that revealed 99 novel missense mutations,of which 21 were classified as damaging mutations through the Poly-Phen2 prediction algorithm.In vitro functional studies were conducted by transient transfection of wild-type and mutant MTHFS into HEK293T cells to determine the impact of the variants on enzyme activity.Results:Of the damaging variants identified in the WES studies,we focused on the gene coding for the enzyme 5,10-methenyl-tetrahydrofolate synthetase(MTHFS).This enzyme catalyzes the production of methenyl THF which is subsequently converted to 5-MTHF.The CFD patient described within was found to carry a homozygous mutation,c.101G>T(p.R34L,rs200058464)in MTHFS,while the parents of the proband are heterozygotes for the MTHFS gene,and the healthy sibling is not a carrier.Conclusion:The mutant allele displayed a 50%reduction in luciferase activity(P<0.05),suggesting that homozygous loss of the MTHFS gene may play a significant role in the development of CFD.展开更多
Understanding the molecular mechanisms of coronavirus disease 2019(COVID-19)pathogenesis and immune response is vital for developing therapies.Single-cell RNA sequencing has been applied to delineate the cellular hete...Understanding the molecular mechanisms of coronavirus disease 2019(COVID-19)pathogenesis and immune response is vital for developing therapies.Single-cell RNA sequencing has been applied to delineate the cellular heterogeneity of the host response toward COVID-19 in multiple tissues and organs.Here,we review the applications and findings from over 80 original COVID-19 single-cell RNA sequencing studies as well as many secondary analysis studies.We describe that single-cell RNA sequencing reveals multiple features of COVID-19 patients with different severity,including cell populations with proportional alteration,COVID-19-induced genes and pathways,severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)infection in single cells,and adaptation of immune repertoire.We also collect published single-cell RNA sequencing datasets from original studies.Finally,we discuss the limitations in current studies and perspectives for future advance.展开更多
Heparan sulfate proteoglycan 2(HSPG2)gene encodes the matrix protein Perlecan,and genetic inactivation of this gene creates mice that are embryonic lethal with severe neural tube defects(NTDs).We discovered rare genet...Heparan sulfate proteoglycan 2(HSPG2)gene encodes the matrix protein Perlecan,and genetic inactivation of this gene creates mice that are embryonic lethal with severe neural tube defects(NTDs).We discovered rare genetic variants of HSPG2 in 10%cases compared to only 4%in controls among a cohort of 369 NTDs.Endorepellin,a peptide cleaved from the domain V of Perlecan,is known to promote angiogenesis and autophagy in endothelial cells.The roles of enderepellin in neurodevelopment remain unclear so far.Our study revealed that endorepellin can migrate to the neuroepithelial cells and then be recognized and bind with the neuroepithelia receptor neurexin in vivo.Through the endocytic pathway,the interaction of endorepellin and neurexin physiologically triggers autophagy and appropriately modulates the differentiation of neural stem cells into neurons as a blocker,which is necessary for normal neural tube closure.We created knock-in(KI)mouse models with human-derived HSPG2 variants,using sperm-like stem cells that had been genetically edited by CRISPR/Cas9.We realized that any HSPG2 variants that affected the function of endorepellin were considered pathogenic causal variants for human NTDs given that the severe NTD phenotypes exhibited by these KI embryos occurred in a significantly higher response frequency compared to wildtype embryos.Our study provides a paradigm for effectively confirming pathogenic mutations in other genetic diseases.Furthermore,we demonstrated that using autophagy inhibitors at a cellular level can repress neuronal differentiation.Therefore,autophagy agonists may prevent NTDs resulting from failed autophagy maintenance and neuronal over-differentiation caused by deleterious endorepellin variants.展开更多
基金supported by the National Key R&D Program of China(2021YFC2701101 to H.W.and X.Y.)the National Natural Science Foundation of China(81930036 and 82150008 to H.W.,and 31000542 to X.Y.)the Commission of Science and Technology of Shanghai Municipality(20JC1418500 to H.W.).
文摘T-box transcription factor T(TBXT;T)is required for mesodermal formation and axial skeletal development.Although it has been extensively studied in various model organisms,human congenital vertebral malformations(CVMs)involving T are not well established.Here,we report a family with 15 CVM patients distributed across 4 generations.All affected individuals carry a heterozygous mutation,T c.596A>G(p.Q199R),which is not found in unaffected family members,indicating co-segregation of the genotype and phenotype.In vitro assays show that T p.Q199R increases the nucleocytoplasmic ratio and enhances its DNA-binding affinity,but reduces its transcriptional activity compared to the wild-type.To determine the pathogenicity of this mutation in vivo,we generated a Q199R knock-in mouse model that recapitulates the human CVM phenotype.Most heterozygous Q199R mice show subtle kinked or shortened tails,while homozygous mice exhibit tail filaments and severe vertebral deformities.Overall,we show that the Q199R mutation in T causes CVM in humans and mice,providing previously unreported evidence supporting the function of T in the genetic etiology of human CVM.
文摘INTRODUCTION Organoids are primary tissue or stem cells derived cell aggregates that have the capacity for self-organization,self-renewal,and the capacity to mimic cellular and tissue level functions.Organoids can overcome the shortcomings of traditional 2D cell culture models and closely mimic 3D primary tissue composition.
文摘Background： Marker detection is an important task in complex disease studies. Here we provide an association rule mining （ARM） based approach for identifying integrated markers through mutual information （MI） based statistically significant feature extraction, and apply it to acute myeloid leukemia （AML） and prostate carcinoma （PC） gene expression and methylation profiles. Methods： We first collect the genes having both expression and methylation values in AML as well as PC. Next, we run Jarque-Bera normality test on the expression/methylation data to divide the whole dataset into two parts： one that follows normal distribution and the other that does not follow normal distribution. Thus, we have now four parts of the dataset： normally distributed expression data, normally distributed methylation data, non-normally distributed expression data, and non-normally distributed methylated data. A feature-extraction technique, ＂mRMR＂ is then utilized on each part. This results in a list of top-ranked genes. Next, we apply Welch t-test （parametric test） and Shrink t-test （non-parametric test） on the expression/methylation data for the top selected normally distributed genes and non-normally distributed genes, respectively. We then use a recent weighted ARM method, ＂RANWAR＂ to combine all/specific resultant genes to generate top oncogenic rules along with respective integrated markers. Finally, we perform literature search as well as KEGG pathway and Gene-Ontology （GO） analyses using Enrichr database for in silico validation of the prioritized oncogenes as the markers and labeling the markers as existing or novel. Results： The novel markers of AML are {ABCB11↑ U KRT17↓} （i.e., ABCBll as up-regulated, ＆ KRT17 as down- regulated）, and {AP1SI-UKRT17↓ U NEIL2-UDYDC1↓}） （i.e., AP1S1 and NEIL2 both as hypo-methylated, ＆ KRT17 and DYDC1 both as down-regulated）. The novel marker of PC is {UBIAD1 ｜｜U APBA2 U C4orf31： （i.e., UBIAD1 as up-regulated and hypo-methylated, ＆ APBA2 and C4orf31 both as down-regulated and hyper- methylated）. Conclusion： The identified novel markers might have critical roles in AML as well as PC. The approach can be applied to other complex disease.
基金partially supported by the National Institutes of Health grants of USA(Grant Nos.R01LM012806,R01DE030122,and R01DE029818)the resource support from Cancer Prevention and Research Institute of Texas of USA(Grant Nos.RP180734 and RP210045)。
文摘Identification of B-cell epitopes(BCEs)plays an essential role in the development of peptide vaccines and immuno-diagnostic reagents,as well as antibody design and production.In this work,we generated a large benchmark dataset comprising 124,879 experimentally supported linear epitope-containing regions in 3567 protein clusters from over 1.3 million B cell assays.Analysis of this curated dataset showed large pathogen diversity covering 176 different families.The accuracy in linear BCE prediction was found to strongly vary with different features,while all sequencederived and structural features were informative.To search more efficient and interpretive feature representations,a ten-layer deep learning framework for linear BCE prediction,namely Net BCE,was developed.Net BCE achieved high accuracy and robust performance with the average area under the curve(AUC)value of 0.8455 in five-fold cross-validation through automatically learning the informative classification features.Net BCE substantially outperformed the conventional machine learning algorithms and other tools,with more than 22.06%improvement of AUC value compared to other tools using an independent dataset.Through investigating the output of important network modules in Net BCE,epitopes and non-epitopes tended to be presented in distinct regions with efficient feature representation along the network layer hierarchy.The Net BCE is freely available at https://github.com/bsml320/Net BCE.
基金supported by National Institutes of Health grants(Grant Nos.R01LM012806R,I01DE030122,and R01DE029818)support from Cancer Prevention and Research Institute of Texas(Grant Nos.CPRIT RP180734 and RP210045),United States.
文摘Single-cell RNA sequencing(scRNA-seq)is revolutionizing the study of complex and dynamic cellular mechanisms.However,cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation,which is cumbersome and subjective.The increasing number of scRNA-seq datasets,as well as numerous published genetic studies,has motivated us to build a comprehensive human cell type reference atlas.Here,we present decoding Cell type Specificity(deCS),an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker genes.We used deCS to annotate scRNAseq data from various tissue types and systematically evaluated the annotation accuracy under different conditions,including reference panels,sequencing depth,and feature selection strategies.Our results demonstrate that expanding the references is critical for improving annotation accuracy.Compared to many existing state-of-the-art annotation tools,deCS significantly reduced computation time and increased accuracy.deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation.Finally,we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits,providing deep insights into the cellular mechanisms underlying disease pathogenesis.
文摘Dear Colleagues,As an Executive Editor-in-Chief,I have edited this Special Issue(SI),entitled “Birth Defects:Issues and Advances in 2022”in the journal Reproductive and Developmental Medicine(RDM,ISSN:2096-2924,CN:10-1442/R),the first ever English journal in the field of reproductive medicine and developmental biology in China's Mainland.Since its launch in 2017,RDM has been dedicated to providing a good platform for academic exchanges among scientists,both at home and abroad.
基金supported by the National Institutes of Health grants (R03DE028103, R03DE027393, and R01LM012806 to Zhongming Zhao, R03DE026208, R03DE026509, R03DE028340, and R01DE026767 to Junichi Iwata, and R01DE030122 and R01DE029818 to Junichi Iwata and Zhongming Zhao)。
文摘Cleft lip with/without cleft palate(CL/P) is one of the most common congenital human birth defects with a prevalence estimated at approximately 1/700 live births worldwide, varying with gender,ethnicity, and geographic location[1]. Significant efforts have been made to understand CL/P pathogenesis.
基金supported by the National Key Research and Development Program of China(2019YFA0801402)the National Natural Science Foundation of China(82271890)+3 种基金the Shanghai Key Clinical Specialty Project(shslczdzk05705)the Shanghai Top Priority Key Discipline Project(2017ZZ02019)Innovative Research Team of High-Level Local Universities in Shanghai(SHSMU-ZDCX20212200)the Macao Science and Technology Development Fund(FDCT)(0092/2022/A2,003/2022/ALC)。
文摘Autosomal recessive spinocerebellar ataxias(SCARs)are one of the most common neurodegenerative diseases characterized by progressive ataxia.Although SCARs are known to be caused by mutations in multiple genes,there are still many cases that go undiagnosed or are misdiagnosed.In this study,we presented a SCAR patient,and identified a probable novel pathogenic mutation(c.1A>G,p.M1V)in the AFG3L2 start codon.The proband's genotype included heterozygous mutations of the compound AFG3L2(p.[M1V];[R632X](c.[1A>G];[1894.C>T])),which were inherited from the father(c.1A>G,p.M1V)and mother(c.1894C>T,p.R632X).Functional studies performed on hi PSCs(human induced pluripotent stem cells)generated from the patients and HEK293T cells showed that the mutations impair mitochondrial function and the unbalanced expression of AFG3L2 mRNA and protein levels.Furthermore,this novel mutation resulted in the degradation of the protein and the reduction of the stability of the AFG3L2 protein,and MCU(mitochondrial calcium uniporter)complex mediated Ca2+overload.
基金supported by the National Key R&D Program of China(2021YFC2701101)the National Natural Science Foundation of China(81930036,82150008,and 81970572)the Commission of Science and Technology of Shanghai Municipality(20JC1418500)。
文摘The challenges and breakthroughs in human genetics can largely depend on the depth of exploring the missing heritability[1]and understanding of genetic variants,which enabled scientists to better elucidate the underlying causes of diseases and apply this knowledge in clinical settings.Human genomes differ from one individual to another in the form of single nucleotide variants(SNVs),small insertions and deletions(indels)(<50 base pairs(bp)),and structural variants(SVs)[2].
基金This work was supported by grants from the National Natural Science Foundation of China(81870459,81970572.Dr.Yun-Ping Lei was supported by NIH grant HD100535,HD098131,and HD083809).
文摘Objective::To investigate the roles of transcription factors (TFs) in the etiology of complex human birth defects, including neural tube defects (NTDs), congenital heart diseases (CHDs), and hypospadias.Methods::We examined the overlap of genetically associated genes among NTDs, CHDs, and hypospadias. We then compared the expression profiles of these diseases based on all the detected genes and disease-associated TFs. The differentially expressed TFs that we obtained were further subjected to functional enrichment analysis to elucidate their role in the development of these birth defects.Results::TF genes were significantly enriched in complex birth defects ( P= 5.95 × 10^(-24)). NTDs, CHDs, and hypospadias showed distinct gene expression profiles compared with the controls. Although TFs could not efficiently separate CHDs from normal subjects, distinct gene expression profiles of TFs could distinguish NTDs and hypospadias from controls. Differentially expressed TFs can be used to characterize NTDs, hypospadias, and controls. The enriched TFs in biological processes (BPs) reflected the different morphological processes of NTDs, CHDs, and hypospadias. Conclusions::This study indicates that abnormal expression patterns of specific TFs may disrupt the normal requirements for developmental equilibrium through the related BPs. The investigation of genetically associated genes and gene expression profiles for the three different complex birth defects provides new insights into how the dysregulation of TFs influences their developmental process.
文摘Objectives:Folates are B vitamins that are essential for several molecular,cellular,and biological processes,including nucleotide synthesis,methylation,and methionine cycling.The physiological impacts of these processes on health also extend to cell proliferation,folate deficiency anemia,and reduction of the risk of birth defects during pregnancy.The primary objective of this study was to characterize the binding affinities of different folate forms,folic acid(FA),5-methyltetrahydrofolate(5MTHF),and folinic acid,to the folate receptorsαandβ,and to the bovine milk folate binding protein.These three dietary forms of folate are found in enriched grains(FA),various fruits and leafy vegetables(folinic acid),and red blood cells(5MTHF).Methods:The half maximal inhibitory concentration values and binding curves of each of these folates for each receptor were determined.Results:Our results indicated that FA had the highest affinity for all folate receptors,followed by 5MTHF,and lastly,by folinic acid,examined by several orders of magnitudes.Conclusion:These data are expected to provide new insights into the therapeutic applications of the different forms of folate in a variety of diseases.
文摘Objective::The prevalence of midline birth defects, such as gastroschisis, has increased worldwide, over the last few decades. This study aims to explore the prevalence, maternal epidemiological characteristics, and natural history of neonates affected by gastroschisis at the University Hospital of Leon city, Nicaragua.Methods:Data were collected from the birth defect surveillance system of the Hospital Oscar Danilo Rosales (HEODRA). The analysis included all pregnancies that had gastroschisis complications between January 1 and December 31, 2020. The prevalence of gastroschisis was calculated according to maternal age. The mothers were interviewed, and the clinical records of the newborns were reviewed.Results::Among the 4,460 deliveries included in this study, four cases of gastroschisis were identified, including three live births and one stillbirth. The gastroschisis rate was 8.9 per 10,000 live births (95% confidence interval [CI]: 0.18-17.8). The prevalence among mothers younger than 20 years and those older than 20 years was 26.4 (95% CI: -3.43 to 56.25) and 3.01 (95% CI: 2.89-8.90)/10,000 births, respectively. Mothers of gastroschisis-affected fetuses were of rural origin ( n = 3), had normal body mass indexes ( n = 3), were exposed to tobacco and wood smoke ( n = 2), and one was exposed to pesticides during the periconceptional period. Primary closure of the gastroschisis was performed on one patient, and complex gastroschisis for intestinal perforation was observed in another patient. The mean hospitalization duration was 33 days, and two patients were discharged alive. Conclusions::Gastroschisis was a significant birth defect among children delivered at HEODRA in 2020. Its prevalence in Nicaragua was higher than that in other countries in the region. All complicated pregnancies were young women with unplanned pregnancies, from rural areas, with exposure to secondhand smoke, and without vitamin supplements before or during the first trimester of pregnancy. Only 67% of infants survived after hospital discharge.
文摘Objective:The purpose of this study was to examine the role of rare variants in the one-carbon metabolic pathway in the etiology of the cerebral folate deficiency(CFD)syndrome.The CFD syndrome is a neurometabolic syndrome identified by low concentrations of 5-methyltetrahydrofolate(5-MTHF)in the cerebrospinal fluid(CSF)in spite of near-normal peripheral folate levels resulting in neurodevelopmental disorders.Methods:The localized folate metabolism impairments in CFD are thought to be either the result of mutations in genes responsible for folate transport or folate turnover through degradation.Genes that have been previously implicated in the etiology of CFD include folate receptor alpha-1(FOLR1),dihydrofolate reductase,proton-coupled folate transporter,and capicua.We performed whole-exome sequencing(WES)analysis of a CFD patient that revealed 99 novel missense mutations,of which 21 were classified as damaging mutations through the Poly-Phen2 prediction algorithm.In vitro functional studies were conducted by transient transfection of wild-type and mutant MTHFS into HEK293T cells to determine the impact of the variants on enzyme activity.Results:Of the damaging variants identified in the WES studies,we focused on the gene coding for the enzyme 5,10-methenyl-tetrahydrofolate synthetase(MTHFS).This enzyme catalyzes the production of methenyl THF which is subsequently converted to 5-MTHF.The CFD patient described within was found to carry a homozygous mutation,c.101G>T(p.R34L,rs200058464)in MTHFS,while the parents of the proband are heterozygotes for the MTHFS gene,and the healthy sibling is not a carrier.Conclusion:The mutant allele displayed a 50%reduction in luciferase activity(P<0.05),suggesting that homozygous loss of the MTHFS gene may play a significant role in the development of CFD.
基金supported by National Institutes of Health grants(R01LM012806,R01DE030122,and R01DE029818)Cancer Prevention and Research Institute of Texas(CPRIT RP180734 and RP210045)The funders had no role in the study design,data collection and analysis,decision to publish,or preparation of the manuscript.Funding for open access charge:CPRIT(RP180734)。
文摘Understanding the molecular mechanisms of coronavirus disease 2019(COVID-19)pathogenesis and immune response is vital for developing therapies.Single-cell RNA sequencing has been applied to delineate the cellular heterogeneity of the host response toward COVID-19 in multiple tissues and organs.Here,we review the applications and findings from over 80 original COVID-19 single-cell RNA sequencing studies as well as many secondary analysis studies.We describe that single-cell RNA sequencing reveals multiple features of COVID-19 patients with different severity,including cell populations with proportional alteration,COVID-19-induced genes and pathways,severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)infection in single cells,and adaptation of immune repertoire.We also collect published single-cell RNA sequencing datasets from original studies.Finally,we discuss the limitations in current studies and perspectives for future advance.
基金supported by the National Key Research and Development Program of China(2021YFC2701100)the National Natural Science Foundation of China(81930036,32293230 and 8215008)+1 种基金the Commission for Science and Technology of Shanghai Municipality(20JC1418500 and 20ZR1404800)Project supported by Shanghai Municipal Science and Technology Major Project。
文摘Heparan sulfate proteoglycan 2(HSPG2)gene encodes the matrix protein Perlecan,and genetic inactivation of this gene creates mice that are embryonic lethal with severe neural tube defects(NTDs).We discovered rare genetic variants of HSPG2 in 10%cases compared to only 4%in controls among a cohort of 369 NTDs.Endorepellin,a peptide cleaved from the domain V of Perlecan,is known to promote angiogenesis and autophagy in endothelial cells.The roles of enderepellin in neurodevelopment remain unclear so far.Our study revealed that endorepellin can migrate to the neuroepithelial cells and then be recognized and bind with the neuroepithelia receptor neurexin in vivo.Through the endocytic pathway,the interaction of endorepellin and neurexin physiologically triggers autophagy and appropriately modulates the differentiation of neural stem cells into neurons as a blocker,which is necessary for normal neural tube closure.We created knock-in(KI)mouse models with human-derived HSPG2 variants,using sperm-like stem cells that had been genetically edited by CRISPR/Cas9.We realized that any HSPG2 variants that affected the function of endorepellin were considered pathogenic causal variants for human NTDs given that the severe NTD phenotypes exhibited by these KI embryos occurred in a significantly higher response frequency compared to wildtype embryos.Our study provides a paradigm for effectively confirming pathogenic mutations in other genetic diseases.Furthermore,we demonstrated that using autophagy inhibitors at a cellular level can repress neuronal differentiation.Therefore,autophagy agonists may prevent NTDs resulting from failed autophagy maintenance and neuronal over-differentiation caused by deleterious endorepellin variants.
