Protein-protein interactions(PPIs)occur when two or more proteins bind together,often resulting in the formation of complexes that perform essential functions within cells.PPIs are crucial for a variety of cellular ac...Protein-protein interactions(PPIs)occur when two or more proteins bind together,often resulting in the formation of complexes that perform essential functions within cells.PPIs are crucial for a variety of cellular activities,including signal transduction,metabolism,and immune response,which makes large-scale identification of PPIs a primary focus of modern biological research(Ge et al.,2003).展开更多
The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".Long-read sequencing(LRS)technol...The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".Long-read sequencing(LRS)technologies are revolutionizing the field of genomics by providing unprecedented insights into genome architecture and function.With the ability to read long fragments of DNA and RNA,LRS overcomes many of the limitations of short-read sequencing,offering a more comprehensive view of genomic,epigenomic,and transcriptomic variations.This technological leap has opened up new avenues for research in diverse biomedical fields.Despite significant progress,there remains a critical need for new experimental methodologies for harnessing LRS technologies,new computational tools for interpreting LRS data,and demonstration of their applications to basic,translational,and clinical research.展开更多
The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".Long-read sequencing(LRS)technol...The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".Long-read sequencing(LRS)technologies are revolutionizing the field of genomics by providing unprecedented insights into genome architecture and function.展开更多
The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of“Long-read Sequencing”.Long-read sequencing(LRS)technologies ar...The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of“Long-read Sequencing”.Long-read sequencing(LRS)technologies are revolutionizing the field of genomics by providing unprecedented insights into genome architecture and function.展开更多
Otoancorin(OTOA)is a glycosylphosphatidylinositol(GPI)-anchored protein mediating the attachment of the tectorial membrane(TM)to the spiral limbus(SL)in the inner ear.Homozygous or compound heterozygous mutations in O...Otoancorin(OTOA)is a glycosylphosphatidylinositol(GPI)-anchored protein mediating the attachment of the tectorial membrane(TM)to the spiral limbus(SL)in the inner ear.Homozygous or compound heterozygous mutations in OTOA cause autosomal recessive deafness(DFNB22).We performed short-read exome sequencing(SRS)in a 10-monthold boy with sensorineural hearing loss,identifying a potential p.Glu787*variant in OTOA.Interestingly,this variant is common among normal-hearing individuals,leading us to question its pathogenic potential.展开更多
The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".
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
Over 17 and 160 types of chemical modifications have been identified in DNA and RNA,respectively.The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edge...Over 17 and 160 types of chemical modifications have been identified in DNA and RNA,respectively.The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics.Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study.Here,we review the recent technological advances in this rapidly evolving field.We focus on high-throughput detection methods and biological findings for these modifications,and discuss questions to be addressed as well.We also summarize third-generation sequencing methods,which enable long-read and single-molecule sequencing of DNA and RNA modification.展开更多
基金supported by Biological Breeding-National Science and Technology Major Project(Grant No.2023ZD040662)National Key R&D Program of China(Grant No.2024YFF1000600)+3 种基金Zhejiang Provincial Natural Science Foundation(Grant No.LQN25C130011,LY23C130004)Natural Science Foundation of China(Grant No.32472115,U22A20456 and W2412006)Major Program of Natural Science Foundation of Zhejiang(Grant No.LD24C130001)ASTIP program of CAAS。
文摘Protein-protein interactions(PPIs)occur when two or more proteins bind together,often resulting in the formation of complexes that perform essential functions within cells.PPIs are crucial for a variety of cellular activities,including signal transduction,metabolism,and immune response,which makes large-scale identification of PPIs a primary focus of modern biological research(Ge et al.,2003).
文摘The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".Long-read sequencing(LRS)technologies are revolutionizing the field of genomics by providing unprecedented insights into genome architecture and function.With the ability to read long fragments of DNA and RNA,LRS overcomes many of the limitations of short-read sequencing,offering a more comprehensive view of genomic,epigenomic,and transcriptomic variations.This technological leap has opened up new avenues for research in diverse biomedical fields.Despite significant progress,there remains a critical need for new experimental methodologies for harnessing LRS technologies,new computational tools for interpreting LRS data,and demonstration of their applications to basic,translational,and clinical research.
文摘The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".Long-read sequencing(LRS)technologies are revolutionizing the field of genomics by providing unprecedented insights into genome architecture and function.
文摘The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of“Long-read Sequencing”.Long-read sequencing(LRS)technologies are revolutionizing the field of genomics by providing unprecedented insights into genome architecture and function.
基金supported by the National Research Foundation of Korea(NRF)grant funded by the Korean government(MSIT)(No.2021R1C1C1007980 to B.J.K.)Chungnam National University Sejong Hospital Research Fund,2022,and Chungnam National University(to B.J.K.)+6 种基金supported by the Basic Science Research Program through the NRF,funded by the Ministry of Education(No.2021R1A2C2092038 to B.Y.C.)Bio Core Facility Center program(No.NRF-2022M3A9G1014007 to B.Y.C.)the Basic Research Laboratory program through the NRF,funded by the Ministry of Education(No.RS-2023-0021971031482092640001 to B.Y.C.)the Technology Innovation Program(No.K_G012002572001 to B.Y.C.)funded By the Ministry of Trade,Industry&Energy(MOTIE,Korea)funded by SNUBH(Seoul National University Bundang Hospital)intramural research fund(No.13-2022-0010,02-2017-0060,16-2023-0002,13-2023-0002,16-2022-0005,13-2024-0004,and 13-2017-0013 to B.Y.C.)supported by the National Institute on Deafness and Other Communication Disorders(NIDCD)part of the US National Institutes of Health(No.R01DC018814 to S.P.).
文摘Otoancorin(OTOA)is a glycosylphosphatidylinositol(GPI)-anchored protein mediating the attachment of the tectorial membrane(TM)to the spiral limbus(SL)in the inner ear.Homozygous or compound heterozygous mutations in OTOA cause autosomal recessive deafness(DFNB22).We performed short-read exome sequencing(SRS)in a 10-monthold boy with sensorineural hearing loss,identifying a potential p.Glu787*variant in OTOA.Interestingly,this variant is common among normal-hearing individuals,leading us to question its pathogenic potential.
文摘The journal Genomics,Proteomics&Bioinformatics(GPB)is inviting submissions for a special issue(to be published in the Spring of 2026)on the topic of"Long-read Sequencing".
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This work was supported by the National Natural Science Foundation of China(Grant No.31861143026 to C.Y.)the Ministry of Science and Technology of China(Grant Nos.2019YFA0110902 and 2019YFA08002501 to C.Y.)the Ludwig Institute for Cancer Research(C-X.S.),Cancer Research UK(C63763/A26394 and C63763/A27122 to C-X.S.)NIHR Oxford Biomedical Research Centre(to C-X.S.)and Emerson Collective(to C-X.S.).L-Y.Z.is supported by China Scholarship Council.The views expressed are those of the authors and not necessarily those of the NHS,the NIHR or the Department of Health.We apologize for not being able to cite all the publications related to this topic due to space constraints of the journal.
文摘Over 17 and 160 types of chemical modifications have been identified in DNA and RNA,respectively.The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics.Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study.Here,we review the recent technological advances in this rapidly evolving field.We focus on high-throughput detection methods and biological findings for these modifications,and discuss questions to be addressed as well.We also summarize third-generation sequencing methods,which enable long-read and single-molecule sequencing of DNA and RNA modification.
