AIM:To identify a maculopathy patient caused by new recessive compound heterozygous variants in RP1L1.METHODS:Comprehensive retinal morphological and functional examinations were evaluated for the patient with RP1L1 m...AIM:To identify a maculopathy patient caused by new recessive compound heterozygous variants in RP1L1.METHODS:Comprehensive retinal morphological and functional examinations were evaluated for the patient with RP1L1 maculopathy.Targeted sequence capture array technique was used to screen potential pathologic variants.Polymerase chain reaction and Sanger sequencing were used to confirm the screening results.RESULTS:Fundus examination showed round macular lesions appeared in both eyes.Optical coherence tomography showed that the inner segment/outer segment continuity was disorganized and disruptive in the left eye,but it was uneven and slightly elevated in the right eye.Fundus autofluorescence showed patchy hyper-autofluorescence in the macula.Visual field examination indicates central defects in both eyes.Electroretinogram(ERG)and multifocal ERG showed no obvious abnormalities.Fundus fluorescein angiography in the macula showed obviously irregular hyper-fluorescence in the right eye and slightly hyper-fluorescence in the left eye.We found that the proband carried a missense variant(c.1972C>T)and a deletion variant(c.4717_4718del)of RP1L1,which were originated from the parents and formed compound heterozygous variants.Both variants are likely pathogenic according to the ACMG criteria.Multimodal imaging,ERG and detailed medical history are important diagnostic tools for differentiating between acquired and inherited retinal disorders.CONCLUSION:A maculopathy case with detailed retinal phenotype and new recessive compound heterozygous variants of RP1L1 is identified in a Chinese family,which expands the understanding of phenotype and genotype in RP1L1 maculopathy.展开更多
Cancer progression involves the sonic hedgehog(SHH)pathway,in which the receptor PTCH1 actives the downstream pathways.Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome(NBCCs)including neoplastic d...Cancer progression involves the sonic hedgehog(SHH)pathway,in which the receptor PTCH1 actives the downstream pathways.Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome(NBCCs)including neoplastic disease and congenital disorder.To evaluate the relationship between PTCH1 and cancer,we applied the CRISPR/Cas9 system to knock out PTCH1 in oral nontumorous epithelial cells(GMSM-K).Then we screened six PTCH1 variants associated with cleft lip/palate(CL/P),one of the congenital disorders in NBCCs,and generated PTCH1 variant and wild-type recombinant PTCH1^(−/−)GMSM-K cell lines.Transcriptome sequencing was conducted in these cell lines.The results revealed that differentially expressed genes(DEGs)in PTCH1^(−/−)GMSM-K were enriched in extracellular compartments,contributing epithelial diseases by pathway enrichment analysis.RT-PCR confirmed that KRT34,KRT81,KRT86,PDGFB,and WNT10B genes,associated with extracellular compartments were highly expressed in PTCH1^(−/−).The Kyoto Encyclopedia of Genes and Genomes analysis also suggested that DEGs are closely related to focal adhesion,transcriptional misregulation,and proteoglycans in breast and gastric cancers.Comparative analysis of samples revealed that the CL/P-associated PTCH1 variants A443G and V908G are potentially carcinogenic.These findings provide new insights into the carcinogenic potential of PTCH1 dysfunction.展开更多
目的研究AIFM1基因突变对Harlequin小鼠年龄相关耳蜗听觉功能的影响。方法用圆窗记录耳蜗电图来评价2月龄和6月龄野生型(WT)和AIFM1基因突变型(KO)Harlequin小鼠的耳蜗外周听觉功能,通过Phalloi-din荧光标记耳蜗基底膜外毛细胞的表皮板...目的研究AIFM1基因突变对Harlequin小鼠年龄相关耳蜗听觉功能的影响。方法用圆窗记录耳蜗电图来评价2月龄和6月龄野生型(WT)和AIFM1基因突变型(KO)Harlequin小鼠的耳蜗外周听觉功能,通过Phalloi-din荧光标记耳蜗基底膜外毛细胞的表皮板来评估毛细胞的损失程度。结果 (1)2月龄组WT型和KO型小鼠的复合动作电位阈值分别为18.6±1.6 d B SPL(n=6)和22.2±2.2 d B SPL(n=6),两组之间没有统计学差异(t=1.282,P>0.05);6个月组WT型和KO型复合动作电位阈值分别为25.7±1.7 d B SPL(n=6)和42.1±3.6 d B SPL(n=6),两组之间差异有统计学意义t=4.129,P<0.01)。(2)2月龄组WT型和KO型小鼠CAP的幅值没有统计学差异(P>0.01),而6个月组的CAP的幅值在高频段(30,35和40 k Hz)有统计学差异(Two-way ANOVA,P<0.05),在低频和中频则没有明显差异。2月龄组和6月龄组WT型和KO型小鼠10 k Hz以下CM的幅值的差异没有统计学意义(P>0.05)。(3)耳蜗外毛细胞计数的结果显示,2月龄组的WT型(n=5)和KO型小鼠(n=5)之间没有统计学差异,而6月龄组的KO型小鼠的耳蜗外毛细胞个数在底回较WT型小鼠明显受损(t=15.1,P<0.0001)。结论 AIFM1基因突变导致Harlequin小鼠耳蜗基底膜底回末端外毛细胞受损,从而导致耳蜗外周听觉功能高频段受损。展开更多
The goal of this study was to identify MSX1 gene variants in multiple Chinese families with nonsyndromic oligodontia and analyse the functional influence of these variants.Whole-exome sequencing(WES)and Sanger sequenc...The goal of this study was to identify MSX1 gene variants in multiple Chinese families with nonsyndromic oligodontia and analyse the functional influence of these variants.Whole-exome sequencing(WES)and Sanger sequencing were performed to identify the causal gene variants in five families with nonsyndromic oligodontia,and a series of bioinformatics databases were used for variant confirmation and functional prediction.Phenotypic characterization of the members of these families was described,and an in vitro analysis was performed for functional evaluation.Five novel MSX1 heterozygous variants were identified:three missense variants[c.662A>C(p.Q221P),c.670C>T(p.R224C),and c.809C>T(p.S270L)],one nonsense variant[c.364G>T(p.G122*)],and one frameshift variant[c.277delG(p.A93Rfs*67)].Preliminary in vitro studies demonstrated that the subcellular localization of MSX1 was abnormal with the p.Q221P,p.R224C,p.G122*,and p.A93Rfs*67 variants compared to the wild type.Three variants(p.Q221P,p.G122*,and p.A93Rfs*67)were classified as pathogenic or likely pathogenic,while p.S270L and p.R224C were of uncertain significance in the current data.Moreover,we summarized and analysed the MSX1-related tooth agenesis positions and found that the type and variant locus were not related to the severity of tooth loss.Our results expand the variant spectrum of nonsyndromic oligodontia and provide valuable information for genetic counselling.展开更多
Long noncoding RNA(lncRNA) HOTAIR and MALAT1 are implicated in the development of multiple cancers. Genetic variants within HOTAIR and MALAT1 may affect the gene expression, thereby modifying genetic susceptibility to...Long noncoding RNA(lncRNA) HOTAIR and MALAT1 are implicated in the development of multiple cancers. Genetic variants within HOTAIR and MALAT1 may affect the gene expression, thereby modifying genetic susceptibility to cervical cancer. A case-control study was designed, including 1 486 cervical cancer patients and 1 536 healthy controls. Based on RegulomeDB database, 11 SNPs were selected and genotyped by using Sequenom’s Mass ARRAY. Univariate and multivariate logistic regression models were used to calculate the odds ratio(OR) and 95% confidence interval(CI). We found that the A allele of rs35643724 in HOTAIR was associated with increased risk of cervical cancer, while the C allele of rs1787666 in MALAT1 was associated with decreased risk. Compared to individuals with 0–1 unfavorable allele, those with 3–4 unfavorable alleles showed18% increased odds of having cervical cancer. Our findings suggest that HOTAIR rs35643724 and MALAT1 rs1787666 might represent potential biomarkers for cervical cancer susceptibility.展开更多
Genetic variants in glioma tumor suppressor candidate region gene 1 （GLTSCR1） and ATM serine/threonine kinase （ATM） have been associated with various cancer risks. Epidemiological studies also revealed the associa...Genetic variants in glioma tumor suppressor candidate region gene 1 （GLTSCR1） and ATM serine/threonine kinase （ATM） have been associated with various cancer risks. Epidemiological studies also revealed the association of variants of GLTSCR1 and ATM genes with different brain tumors. However, little is known about the relationship between both gene polymorphisms and lung cancer risk. We conducted a Chinese hospital-based casecontrol study involving 384 lung cancer cases and 387 cancer-free controls. No significant differences in the single polymorphism （GLTSCR1 rs1035938 and ATM rs11212592） association were found in five genetic models （co-dominant, dominant, recessive, overdominant and log-additive models） （adjusted by smoking duration）. Join effect of three SNPs （PPPIR13L rs1970764, CD3EAP rs967591, GLTSCR1 rs1035938） on chromosome 19q 13.3 showed that the designated haplotype2 （rs 1970764 G-rs967591 A-rs 1035938 C） [OR （95% CI）=1.60 （1.11-2.32）, P=0.012] and haplotype8 （rs 1970764 G-rs967591 G-rs 1035938 T） [OR （95% CI）=2.45 （1.17-5.12）, P=0.018] were associated with increased risk of lung cancer （adjusted by smoking duration）. The analysis ofmultifactor dimensionality reduction revealed that two 3-way models were the best fit models in analyses of 2 loci （P〈0.001） or 4 loci （P=0.015-0.016）. The entropy-based analysis indicated the strongest synergistic effect between PPPIR13L rs1970764 and ATM rs11212592 in analysis of four genes. In conclusion, our study suggests that haplotypes consisting of PPPIR13L rs1970764- CD3EAP rs967591-GLTSCR1 rs1035938 on Chr19q13.3, interaction of smoking and GLTSCR1 rs1035938-ATM rs11212592, and synergistic action of PPPIR13L rs1970764 and ATM rs 11212592 may associate with lung cancer risk in the Chinese population.展开更多
AIM:To detect the pathogenic gene variant in a family with neurofibromatosis type 1(NF1).METHODS:This patient with NF1 was sequenced using target sequence capture and high-throughput sequencing technology.After detect...AIM:To detect the pathogenic gene variant in a family with neurofibromatosis type 1(NF1).METHODS:This patient with NF1 was sequenced using target sequence capture and high-throughput sequencing technology.After detecting the suspicious pathogenic variant type,the pathogenic variant sites of the patient and the patient’s family members were verified by multiple ligation dependent probe amplification and Sanger sequencing.Sift,polyphen-2,Mutation Taster and GERP++software were used to predict the pathogenicity of the unknown loci.The clinical data,diagnosis and treatment process of the patients were reviewed.Using the keyword“NF1;frameshift pathogenic variant”,relevant literature was gathered for analysis from Chinese and international databases,with articles dating from the establishment of each database to April 2022.RESULTS:A heterozygous frameshift pathogenic variant of NF1 in exon 33 was detected in the patient.The insertion of adenine in coding region 4486 resulted in the replacement of isoleucine with asparagine in protein 1497.Sanger sequencing validation and segregation analysis were performed,which demonstrated that the NF1 gene was cosegregated with the disease phenotype in this family.This study identified a novel NF1 heterozygous frameshift mutation c.4486dupA(p.I1497Nfs*12).Relevant literature retrieval found 7 Chinese articles and 12 foreign articles.With NF1 gene mutation,mutation types are diverse,including point mutation,frameshift mutation,splice site mutation,exon mutation,chimeric mutation and de novo mutation.Foreign reports are based on autosomal dominant inheritance.CONCLUSION:This study’s results demonstrate that a novel deletion in exon 33 caused NF1 in this Chinese family,expanding the mutational spectrum of the NF1 gene.展开更多
基金Supported by Shenzhen Science and Technology Program,Shenzhen,China(No.JCYJ20200109145001814,No.SGDX20211123120001001)the National Natural Science Foundation of China(No.81970790)Sanming Project of Medicine in Shenzhen(No.SZSM202011015).
文摘AIM:To identify a maculopathy patient caused by new recessive compound heterozygous variants in RP1L1.METHODS:Comprehensive retinal morphological and functional examinations were evaluated for the patient with RP1L1 maculopathy.Targeted sequence capture array technique was used to screen potential pathologic variants.Polymerase chain reaction and Sanger sequencing were used to confirm the screening results.RESULTS:Fundus examination showed round macular lesions appeared in both eyes.Optical coherence tomography showed that the inner segment/outer segment continuity was disorganized and disruptive in the left eye,but it was uneven and slightly elevated in the right eye.Fundus autofluorescence showed patchy hyper-autofluorescence in the macula.Visual field examination indicates central defects in both eyes.Electroretinogram(ERG)and multifocal ERG showed no obvious abnormalities.Fundus fluorescein angiography in the macula showed obviously irregular hyper-fluorescence in the right eye and slightly hyper-fluorescence in the left eye.We found that the proband carried a missense variant(c.1972C>T)and a deletion variant(c.4717_4718del)of RP1L1,which were originated from the parents and formed compound heterozygous variants.Both variants are likely pathogenic according to the ACMG criteria.Multimodal imaging,ERG and detailed medical history are important diagnostic tools for differentiating between acquired and inherited retinal disorders.CONCLUSION:A maculopathy case with detailed retinal phenotype and new recessive compound heterozygous variants of RP1L1 is identified in a Chinese family,which expands the understanding of phenotype and genotype in RP1L1 maculopathy.
基金This work was supported by the Natural Science Foundation of China(Nos.81870747,82170916)Clinical Medicine Plus X–Young Scholars Project(PKU2021LCXQ003)the Fundamental Research Funds for the Central Universities(BMU2021YJ001).
文摘Cancer progression involves the sonic hedgehog(SHH)pathway,in which the receptor PTCH1 actives the downstream pathways.Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome(NBCCs)including neoplastic disease and congenital disorder.To evaluate the relationship between PTCH1 and cancer,we applied the CRISPR/Cas9 system to knock out PTCH1 in oral nontumorous epithelial cells(GMSM-K).Then we screened six PTCH1 variants associated with cleft lip/palate(CL/P),one of the congenital disorders in NBCCs,and generated PTCH1 variant and wild-type recombinant PTCH1^(−/−)GMSM-K cell lines.Transcriptome sequencing was conducted in these cell lines.The results revealed that differentially expressed genes(DEGs)in PTCH1^(−/−)GMSM-K were enriched in extracellular compartments,contributing epithelial diseases by pathway enrichment analysis.RT-PCR confirmed that KRT34,KRT81,KRT86,PDGFB,and WNT10B genes,associated with extracellular compartments were highly expressed in PTCH1^(−/−).The Kyoto Encyclopedia of Genes and Genomes analysis also suggested that DEGs are closely related to focal adhesion,transcriptional misregulation,and proteoglycans in breast and gastric cancers.Comparative analysis of samples revealed that the CL/P-associated PTCH1 variants A443G and V908G are potentially carcinogenic.These findings provide new insights into the carcinogenic potential of PTCH1 dysfunction.
文摘目的研究AIFM1基因突变对Harlequin小鼠年龄相关耳蜗听觉功能的影响。方法用圆窗记录耳蜗电图来评价2月龄和6月龄野生型(WT)和AIFM1基因突变型(KO)Harlequin小鼠的耳蜗外周听觉功能,通过Phalloi-din荧光标记耳蜗基底膜外毛细胞的表皮板来评估毛细胞的损失程度。结果 (1)2月龄组WT型和KO型小鼠的复合动作电位阈值分别为18.6±1.6 d B SPL(n=6)和22.2±2.2 d B SPL(n=6),两组之间没有统计学差异(t=1.282,P>0.05);6个月组WT型和KO型复合动作电位阈值分别为25.7±1.7 d B SPL(n=6)和42.1±3.6 d B SPL(n=6),两组之间差异有统计学意义t=4.129,P<0.01)。(2)2月龄组WT型和KO型小鼠CAP的幅值没有统计学差异(P>0.01),而6个月组的CAP的幅值在高频段(30,35和40 k Hz)有统计学差异(Two-way ANOVA,P<0.05),在低频和中频则没有明显差异。2月龄组和6月龄组WT型和KO型小鼠10 k Hz以下CM的幅值的差异没有统计学意义(P>0.05)。(3)耳蜗外毛细胞计数的结果显示,2月龄组的WT型(n=5)和KO型小鼠(n=5)之间没有统计学差异,而6月龄组的KO型小鼠的耳蜗外毛细胞个数在底回较WT型小鼠明显受损(t=15.1,P<0.0001)。结论 AIFM1基因突变导致Harlequin小鼠耳蜗基底膜底回末端外毛细胞受损,从而导致耳蜗外周听觉功能高频段受损。
基金supported by the National Natural Science Foundation of China(81970902,81771054,and 81600846).
文摘The goal of this study was to identify MSX1 gene variants in multiple Chinese families with nonsyndromic oligodontia and analyse the functional influence of these variants.Whole-exome sequencing(WES)and Sanger sequencing were performed to identify the causal gene variants in five families with nonsyndromic oligodontia,and a series of bioinformatics databases were used for variant confirmation and functional prediction.Phenotypic characterization of the members of these families was described,and an in vitro analysis was performed for functional evaluation.Five novel MSX1 heterozygous variants were identified:three missense variants[c.662A>C(p.Q221P),c.670C>T(p.R224C),and c.809C>T(p.S270L)],one nonsense variant[c.364G>T(p.G122*)],and one frameshift variant[c.277delG(p.A93Rfs*67)].Preliminary in vitro studies demonstrated that the subcellular localization of MSX1 was abnormal with the p.Q221P,p.R224C,p.G122*,and p.A93Rfs*67 variants compared to the wild type.Three variants(p.Q221P,p.G122*,and p.A93Rfs*67)were classified as pathogenic or likely pathogenic,while p.S270L and p.R224C were of uncertain significance in the current data.Moreover,we summarized and analysed the MSX1-related tooth agenesis positions and found that the type and variant locus were not related to the severity of tooth loss.Our results expand the variant spectrum of nonsyndromic oligodontia and provide valuable information for genetic counselling.
基金supported by National Natural Science Foundation of China(81502873)the Natural Science Foundation of Jiangsu Province(BK20150997)+3 种基金Priority Academic Program for the Development of Jiangsu Higher Education Institutions(Public Health and Preventive Medicine)Innovation Fund of State key Laboratory of Reproductive Medicine(SKLRMGC201802)Clinical Medicine Research Fund of the Chinese Medical Association(17020420711)Top-notch Academic Programs Project of Jiangsu Higher Education Institutions(PPZY2015A067)
文摘Long noncoding RNA(lncRNA) HOTAIR and MALAT1 are implicated in the development of multiple cancers. Genetic variants within HOTAIR and MALAT1 may affect the gene expression, thereby modifying genetic susceptibility to cervical cancer. A case-control study was designed, including 1 486 cervical cancer patients and 1 536 healthy controls. Based on RegulomeDB database, 11 SNPs were selected and genotyped by using Sequenom’s Mass ARRAY. Univariate and multivariate logistic regression models were used to calculate the odds ratio(OR) and 95% confidence interval(CI). We found that the A allele of rs35643724 in HOTAIR was associated with increased risk of cervical cancer, while the C allele of rs1787666 in MALAT1 was associated with decreased risk. Compared to individuals with 0–1 unfavorable allele, those with 3–4 unfavorable alleles showed18% increased odds of having cervical cancer. Our findings suggest that HOTAIR rs35643724 and MALAT1 rs1787666 might represent potential biomarkers for cervical cancer susceptibility.
基金This study was funded by the National Natural Science Foundation of China （No. 30571016 and No. 81072384）.
文摘Genetic variants in glioma tumor suppressor candidate region gene 1 （GLTSCR1） and ATM serine/threonine kinase （ATM） have been associated with various cancer risks. Epidemiological studies also revealed the association of variants of GLTSCR1 and ATM genes with different brain tumors. However, little is known about the relationship between both gene polymorphisms and lung cancer risk. We conducted a Chinese hospital-based casecontrol study involving 384 lung cancer cases and 387 cancer-free controls. No significant differences in the single polymorphism （GLTSCR1 rs1035938 and ATM rs11212592） association were found in five genetic models （co-dominant, dominant, recessive, overdominant and log-additive models） （adjusted by smoking duration）. Join effect of three SNPs （PPPIR13L rs1970764, CD3EAP rs967591, GLTSCR1 rs1035938） on chromosome 19q 13.3 showed that the designated haplotype2 （rs 1970764 G-rs967591 A-rs 1035938 C） [OR （95% CI）=1.60 （1.11-2.32）, P=0.012] and haplotype8 （rs 1970764 G-rs967591 G-rs 1035938 T） [OR （95% CI）=2.45 （1.17-5.12）, P=0.018] were associated with increased risk of lung cancer （adjusted by smoking duration）. The analysis ofmultifactor dimensionality reduction revealed that two 3-way models were the best fit models in analyses of 2 loci （P〈0.001） or 4 loci （P=0.015-0.016）. The entropy-based analysis indicated the strongest synergistic effect between PPPIR13L rs1970764 and ATM rs11212592 in analysis of four genes. In conclusion, our study suggests that haplotypes consisting of PPPIR13L rs1970764- CD3EAP rs967591-GLTSCR1 rs1035938 on Chr19q13.3, interaction of smoking and GLTSCR1 rs1035938-ATM rs11212592, and synergistic action of PPPIR13L rs1970764 and ATM rs 11212592 may associate with lung cancer risk in the Chinese population.
基金Supported by National High Level Hospital Clinical Research Funding(No.2022-PUMCH-A-031)。
文摘AIM:To detect the pathogenic gene variant in a family with neurofibromatosis type 1(NF1).METHODS:This patient with NF1 was sequenced using target sequence capture and high-throughput sequencing technology.After detecting the suspicious pathogenic variant type,the pathogenic variant sites of the patient and the patient’s family members were verified by multiple ligation dependent probe amplification and Sanger sequencing.Sift,polyphen-2,Mutation Taster and GERP++software were used to predict the pathogenicity of the unknown loci.The clinical data,diagnosis and treatment process of the patients were reviewed.Using the keyword“NF1;frameshift pathogenic variant”,relevant literature was gathered for analysis from Chinese and international databases,with articles dating from the establishment of each database to April 2022.RESULTS:A heterozygous frameshift pathogenic variant of NF1 in exon 33 was detected in the patient.The insertion of adenine in coding region 4486 resulted in the replacement of isoleucine with asparagine in protein 1497.Sanger sequencing validation and segregation analysis were performed,which demonstrated that the NF1 gene was cosegregated with the disease phenotype in this family.This study identified a novel NF1 heterozygous frameshift mutation c.4486dupA(p.I1497Nfs*12).Relevant literature retrieval found 7 Chinese articles and 12 foreign articles.With NF1 gene mutation,mutation types are diverse,including point mutation,frameshift mutation,splice site mutation,exon mutation,chimeric mutation and de novo mutation.Foreign reports are based on autosomal dominant inheritance.CONCLUSION:This study’s results demonstrate that a novel deletion in exon 33 caused NF1 in this Chinese family,expanding the mutational spectrum of the NF1 gene.
