Aberrant RNA alternative splicing in cancer generates varied novel isoforms and protein variants that facilitate cancer progression.Here,we employed the advanced long-read full-length transcriptome sequencing on gallb...Aberrant RNA alternative splicing in cancer generates varied novel isoforms and protein variants that facilitate cancer progression.Here,we employed the advanced long-read full-length transcriptome sequencing on gallbladder normal tissues,tumors,and cell lines to establish a comprehensive full-length gallbladder transcriptomic atlas.It is of note that receptor tyrosine kinases were one of the most dynamic components with highly variable transcript,with Erb-B2 receptor tyrosine kinase 2(ERBB2)as a prime representative.A novel transcript,designated ERBB2 i14e,was identified for encoding a novel functional protein,and its protein expression was elevated in gallbladder cancer and strongly associated with worse prognosis.With the regulation of splicing factors ESRP1/2,ERBB2 i14e was alternatively spliced from intron 14 and the encoded i14e peptide was proved to facilitate the interaction with ERBB3 and downstream signaling activation of AKT.ERBB2 i14e was inducible and its expression attenuated anti-ERBB2 treatment efficacy in tumor xenografts.Further studies with patient derived xenografts models validated that ERBB2 i14e blockage with antisense oligonucleotide enhanced the tumor sensitivity to trastuzumab and its drug conjugates.Overall,this study provides a gallbladder specific long-read transcriptome profile and discovers a novel mechanism of trastuzumab resistance,thus ultimately devising strategies to improve trastuzumab therapy.展开更多
Objective:To report a fetus with ARCN1-related syndrome caused by a novel de novo heterozygous variant,highlighting the importance of early genetic diagnosis in prenatal care.Methods:The clinical and genetic data of a...Objective:To report a fetus with ARCN1-related syndrome caused by a novel de novo heterozygous variant,highlighting the importance of early genetic diagnosis in prenatal care.Methods:The clinical and genetic data of a fetus with a complex combination of clinical signs and a novel de novo heterozygous variant were collected and have been summarized in this study.The potential pathogenic variant was identified throughout the whole exome sequencing and the effects of candidate variants were further validated by a minigene splicing assay.Results:Prenatal systematic ultrasound detected fetal growth restriction.Genetic analysis identified a novel de novo heterozygous variant within the ARCN1 gene—c.1241+5G>A—located in intron 8.In vitro minigene splicing assays demonstrated that the variant led to two abnormal transcripts.The longer transcript retained 189 base pairs of intron 8,resulting in a truncated protein of 414 amino acids(p.Ser415*).The shorter transcript involved exon 8 skippings,producing a truncated protein of 407 amino acids(p.Ile378Serfs*31).Conclusion:A novel de novo heterozygous variant of the ARCN1 gene,namely NM_001655.5:c.1241+5G>A,was discovered and identified in a fetus with rhizomelic short stature,microretrognathia,and developmental delays.展开更多
Targeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases;however, using DNA-based sequencing techniques, the current molecular diagnostic yi...Targeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases;however, using DNA-based sequencing techniques, the current molecular diagnostic yield is at best 50%. In recent years, RNA sequencing has been shown to be able to provide a genetic diagnosis in patients whose conditions were previously unable to be identified by DNA analysis. RNA sequencing can reveal expression outliers, aberrant splicing events, allele-specific expression, and new pathogenic variants, and as such can complement and expand on the traditional genomic methods used to diagnose Mendelian diseases. Therefore, RNA sequencing is expected to become a routine method for genetic diagnosis in the future. This article reviews the applications and challenges of RNA sequencing in the genetic diagnosis of Mendelian diseases.展开更多
基金supported by grants from National Natural Science Foundation of China(No.32130036,82403148,82303937,82073206)Shanghai Shenkang Clinical Technology Innovation Project(No.SHDC12021101)+8 种基金Basic Research Project of Science and Technology Commission of Shanghai Municipality(No.20JC1419100)National Key Research and Development Program of China(No.2021YFE0203300)Science and Technology Innovation Action Plan Technical Standards Project of Science and Technology Commission of Shanghai Municipality(23DZ2202800)Cooperative Research Projects of Shanghai Jiao Tong University(2022LHA13)Major Science and Technology R&D Project of the Science and Technology Department of Jiangxi Province(20213AAG01013)Shanghai Outstanding Academic Leader(23XD1450700),Shanghai Rising-Star Program(23QA1408500)Young Talents Project of Shanghai Municipal Health Commission(2022YQ061)Shanghai Municipal Health Commission health Industry clinical research special project(No.20224Z0014)the Shuguang Program of Shanghai Education Development Foundation and Shanghai Municipal Education Commission(No.20SG14).
文摘Aberrant RNA alternative splicing in cancer generates varied novel isoforms and protein variants that facilitate cancer progression.Here,we employed the advanced long-read full-length transcriptome sequencing on gallbladder normal tissues,tumors,and cell lines to establish a comprehensive full-length gallbladder transcriptomic atlas.It is of note that receptor tyrosine kinases were one of the most dynamic components with highly variable transcript,with Erb-B2 receptor tyrosine kinase 2(ERBB2)as a prime representative.A novel transcript,designated ERBB2 i14e,was identified for encoding a novel functional protein,and its protein expression was elevated in gallbladder cancer and strongly associated with worse prognosis.With the regulation of splicing factors ESRP1/2,ERBB2 i14e was alternatively spliced from intron 14 and the encoded i14e peptide was proved to facilitate the interaction with ERBB3 and downstream signaling activation of AKT.ERBB2 i14e was inducible and its expression attenuated anti-ERBB2 treatment efficacy in tumor xenografts.Further studies with patient derived xenografts models validated that ERBB2 i14e blockage with antisense oligonucleotide enhanced the tumor sensitivity to trastuzumab and its drug conjugates.Overall,this study provides a gallbladder specific long-read transcriptome profile and discovers a novel mechanism of trastuzumab resistance,thus ultimately devising strategies to improve trastuzumab therapy.
基金supported by grants from the National Natural Science Foundation of China(General Program,No.82171678)the Science,Technology,and Innovation Commission of Shenzhen Municipality(No.JCYJ20200109140614667)+1 种基金the Shenzhen Science and Technology Innovation Program(No.JCYJ20230807143504009)the Natural Science Foundation of Hubei Province(No.2023AFC018).
文摘Objective:To report a fetus with ARCN1-related syndrome caused by a novel de novo heterozygous variant,highlighting the importance of early genetic diagnosis in prenatal care.Methods:The clinical and genetic data of a fetus with a complex combination of clinical signs and a novel de novo heterozygous variant were collected and have been summarized in this study.The potential pathogenic variant was identified throughout the whole exome sequencing and the effects of candidate variants were further validated by a minigene splicing assay.Results:Prenatal systematic ultrasound detected fetal growth restriction.Genetic analysis identified a novel de novo heterozygous variant within the ARCN1 gene—c.1241+5G>A—located in intron 8.In vitro minigene splicing assays demonstrated that the variant led to two abnormal transcripts.The longer transcript retained 189 base pairs of intron 8,resulting in a truncated protein of 414 amino acids(p.Ser415*).The shorter transcript involved exon 8 skippings,producing a truncated protein of 407 amino acids(p.Ile378Serfs*31).Conclusion:A novel de novo heterozygous variant of the ARCN1 gene,namely NM_001655.5:c.1241+5G>A,was discovered and identified in a fetus with rhizomelic short stature,microretrognathia,and developmental delays.
基金This work was supported by the National Key Research and Development Program of China (Nos. 2018YFC1003800, 2017YFC1001500, and 2016YFC1000600)the National Natural Science Foundation of China (Nos. 81725006, 81822019, 81771581, 81971450, and 81971382)+5 种基金Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01)Project of Shanghai Municipal Science and Technology Commission (No. 19JC1411001)the Natural Science Foundation of Shanghai (No. 19ZR1444500)Shuguang Program of Shanghai Education Development Foundation and Shanghai Municipal Education Commission (No. 18SG03)the Foundation of Shanghai Health and Family Planning Commission (No. 20154Y0162)the Capacity Building Planning Program for Shanghai Women and Children’s Health Service, and the Collaborative Innovation Center Project Construction for Shanghai Women and Children’s Health.
文摘Targeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases;however, using DNA-based sequencing techniques, the current molecular diagnostic yield is at best 50%. In recent years, RNA sequencing has been shown to be able to provide a genetic diagnosis in patients whose conditions were previously unable to be identified by DNA analysis. RNA sequencing can reveal expression outliers, aberrant splicing events, allele-specific expression, and new pathogenic variants, and as such can complement and expand on the traditional genomic methods used to diagnose Mendelian diseases. Therefore, RNA sequencing is expected to become a routine method for genetic diagnosis in the future. This article reviews the applications and challenges of RNA sequencing in the genetic diagnosis of Mendelian diseases.
