Dear Editor,Enterovirus 71(EV71)is the main pathogen of hand,foot,and mouth disease(HFMD),which is a serious public health threat,especially in the Asia-Pacific region(Wu et al.,2013).Due to the lack of effective anti...Dear Editor,Enterovirus 71(EV71)is the main pathogen of hand,foot,and mouth disease(HFMD),which is a serious public health threat,especially in the Asia-Pacific region(Wu et al.,2013).Due to the lack of effective antivirals for treatment,supportive therapy remains to be the primary measure for severe infections of EV71.EV71 belongs to the genus Enterovirus in the family of Picornavirridae.EV71 encodes a polyprotein that is proteolytically cleaved into four structural proteins and seven nonstructural proteins,i.e.,VP1 to VP4,2A to 2C,and 3A to 3D.Moreover,an alternative encoding strategy of harboring a novel open reading frame encoding a short peptide has been recently reported in gut epithelial cells infected with some enteroviruses(Lulla et al.,2019).Structural proteins play a key role in the packaging and maturation of virus particles,while non-structural proteins are mainly involved in the replication process of virus.Among them,the 3D polymerase(3Dpol)protein functions as an RNA-dependent RNA polymerase(RdRP)that is essential for viral RNA synthesis(Wu et al.,2010).展开更多
Cervical cancer(CC)is the second most common cancer of female reproductive system.However,satisfactory prognostic model for CC remains to be established.In this study,we perform whole-exome sequencing on formalin-fixe...Cervical cancer(CC)is the second most common cancer of female reproductive system.However,satisfactory prognostic model for CC remains to be established.In this study,we perform whole-exome sequencing on formalin-fixed and paraffin-embedded tumor specimens extracted from 67 recurrent and 28 matched non-recurrent CC patients.As a result,four core mutated genes(i.e.,DCHS2,DNAH10,RYR1,and WDFY4)that are differentially presented in recurrent and non-recurrent CC patients are screened out to construct a recurrence-free related score(RRS)model capable of predicting CC prognosis in our cohort,which is further confirmed in TCGA CESC cohort.Moreover,combining tumor mutational burden(TMB)and RRS into an integrated RRS/TMB model enables better stratification of CC patients with distinct prognosis in both cohorts.Increased infiltration of multiple immune cell types,enriched interferon signaling pathway,and elevated cytolytic activity are evident in tumors from patients with a higher RRS and/or a higher TMB.In summary,this study establishes a novel mutation-based prognostic model for CC,the predictive value of which can be attributable to immunological mechanisms.This study will provide insight into the utilization of mutational analysis in guiding therapeutic strategies for CC patients.展开更多
The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male...The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male individual by using HiFi and Hi-C.We assembled two high-quality haplotypes of the HJ genome(haplotype 1(H1):3.1 Gb,haplotype 2(H2):2.9 Gb).The continuity(H1:contig N50=28.2 Mb,H2:contig N50=25.9 Mb)and completeness(BUSCO:H1=94.9%,H2=93.5%)are substantially better than those of other Chinese genomes,for example,HX1,NH1.0,and YH2.0.By comparing HJ genome with GRCh38,we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2,respectively.In addition,we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2,respectively.Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.展开更多
Glioblastoma multiforme(GBM),defined as IDH-wild-type diffuse gliomas(WHO CNS grade IV),is the most common and aggressive primary brain tumor.1 Age significantly influences GBM,with mutational landscape varied by age....Glioblastoma multiforme(GBM),defined as IDH-wild-type diffuse gliomas(WHO CNS grade IV),is the most common and aggressive primary brain tumor.1 Age significantly influences GBM,with mutational landscape varied by age.2 One of the most significant updates in the 2021 WHO classification is the division of diffuse gliomas into pediatric-type and adult-type gliomas,reflecting the growing understanding of their distinct molecular drivers and prognostic implications.展开更多
基金supported by Hubei Provincial Natural Science Foundation of China(2025AFB822)National Key Research and Development Program of China(No.2022YFD1800100)National Natural Science Foundation of China(32100110).
文摘Dear Editor,Enterovirus 71(EV71)is the main pathogen of hand,foot,and mouth disease(HFMD),which is a serious public health threat,especially in the Asia-Pacific region(Wu et al.,2013).Due to the lack of effective antivirals for treatment,supportive therapy remains to be the primary measure for severe infections of EV71.EV71 belongs to the genus Enterovirus in the family of Picornavirridae.EV71 encodes a polyprotein that is proteolytically cleaved into four structural proteins and seven nonstructural proteins,i.e.,VP1 to VP4,2A to 2C,and 3A to 3D.Moreover,an alternative encoding strategy of harboring a novel open reading frame encoding a short peptide has been recently reported in gut epithelial cells infected with some enteroviruses(Lulla et al.,2019).Structural proteins play a key role in the packaging and maturation of virus particles,while non-structural proteins are mainly involved in the replication process of virus.Among them,the 3D polymerase(3Dpol)protein functions as an RNA-dependent RNA polymerase(RdRP)that is essential for viral RNA synthesis(Wu et al.,2010).
基金supported by the National Key Research and Development Program(2021YFC2701204 to H.W.)the"Jianbing"and"Lingyan"R&D programs of Zhejiang province(2022C03013 to H.W.)+3 种基金the National Natural Science Foundation of China(82373260 to H.W.and 82273211 to Y.H.)the Research Funds from Tongji Hospital(20185BJRC004 and 2019BJRC008 to H.W.)the Fundamental Research Funds for the Central Universities,HUST(2021GCRC073 to X.H.)the Nature Science Foundation of Hubei Province(2021CFB346 to Y.H.).
文摘Cervical cancer(CC)is the second most common cancer of female reproductive system.However,satisfactory prognostic model for CC remains to be established.In this study,we perform whole-exome sequencing on formalin-fixed and paraffin-embedded tumor specimens extracted from 67 recurrent and 28 matched non-recurrent CC patients.As a result,four core mutated genes(i.e.,DCHS2,DNAH10,RYR1,and WDFY4)that are differentially presented in recurrent and non-recurrent CC patients are screened out to construct a recurrence-free related score(RRS)model capable of predicting CC prognosis in our cohort,which is further confirmed in TCGA CESC cohort.Moreover,combining tumor mutational burden(TMB)and RRS into an integrated RRS/TMB model enables better stratification of CC patients with distinct prognosis in both cohorts.Increased infiltration of multiple immune cell types,enriched interferon signaling pathway,and elevated cytolytic activity are evident in tumors from patients with a higher RRS and/or a higher TMB.In summary,this study establishes a novel mutation-based prognostic model for CC,the predictive value of which can be attributable to immunological mechanisms.This study will provide insight into the utilization of mutational analysis in guiding therapeutic strategies for CC patients.
基金the National Key R&D Program of China(2022YFC3400300)the National Natural Science Foundation of China(32125009,62172325,32070663)+1 种基金the National Key R&D Program of China(2017YFC0906501)the Key Construction Program of the National‘985’Project,and the Fundamental Research Funds for the Central Universities.
文摘The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male individual by using HiFi and Hi-C.We assembled two high-quality haplotypes of the HJ genome(haplotype 1(H1):3.1 Gb,haplotype 2(H2):2.9 Gb).The continuity(H1:contig N50=28.2 Mb,H2:contig N50=25.9 Mb)and completeness(BUSCO:H1=94.9%,H2=93.5%)are substantially better than those of other Chinese genomes,for example,HX1,NH1.0,and YH2.0.By comparing HJ genome with GRCh38,we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2,respectively.In addition,we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2,respectively.Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.
基金supported by the National Natural Science Foundation of China(No.82373403 to Y.C.)the Association Foundation Program of Yunnan Provincial Science and Technology Department and Kunming Medical University(China)(No.202001AY070001-160 to P.D.)the Special Grant for High-level Personnel of Yunnan Province,China(No.L-2019020 to P.D.)。
文摘Glioblastoma multiforme(GBM),defined as IDH-wild-type diffuse gliomas(WHO CNS grade IV),is the most common and aggressive primary brain tumor.1 Age significantly influences GBM,with mutational landscape varied by age.2 One of the most significant updates in the 2021 WHO classification is the division of diffuse gliomas into pediatric-type and adult-type gliomas,reflecting the growing understanding of their distinct molecular drivers and prognostic implications.
