Epiboly,the coordinated spreading of the enveloping layer(EVL),the yolk syncytial layer(YSL)and the deep cells(DCs)toward the vegetal pole,is required for gastrulation.Interference with the EVL leads to early developm...Epiboly,the coordinated spreading of the enveloping layer(EVL),the yolk syncytial layer(YSL)and the deep cells(DCs)toward the vegetal pole,is required for gastrulation.Interference with the EVL leads to early developmental failure.However,the genetic factors underlying EVL differentiation are so far unknown.By in-depth analyzing of single-cell sequencing data from 4 h post fertilization zebrafish embryos,we identified 105 genes(FDR<0.05)which showed highly specific EVL expression,among which the transcription factor cebpb and genes(krt18,cldne,cldnb,krt4,krt5)involved in cell-cell junction formation were exclusively expressed in EVL.To explore the role of cebpb in EVL differentiation,we knocked down its expression by morpholino-labeled antisense RNA.The morphant embryos showed disrupted EVL and developmental termination prior to epiboly.In accordance,expression of the EVL specific cell-adhesion molecule genes were significantly reduced.Thus,cebpb is the earliest EVL marker and essential for EVL differentiation in zebrafish.The elucidation of the specific EVL gene set provides us new insights into the molecular mechanisms underlying EVL differentiation.展开更多
Genome-wide association studies(GWASs)have identified over 140 colorectal cancer(CRC)-associated loci;however,target genes at the majority of loci and underlying molecular mechanisms are poorly understood.Here,we util...Genome-wide association studies(GWASs)have identified over 140 colorectal cancer(CRC)-associated loci;however,target genes at the majority of loci and underlying molecular mechanisms are poorly understood.Here,we utilized a Bayesian approach,integrative risk gene selector(iRIGS),to prioritize risk genes at CRC GWAS loci by integrating multi-omics data.As a result,a total of 105 high-confidence risk genes(HRGs)were identified,which exhibited strong gene dependencies for CRC and enrichment in the biological processes implicated in CRC.Among the 105 HRGs,CEBPB,located at the 20q13.13 locus,acted as a transcription factor playing critical roles in cancer.Our subsequent assays indicated the tumor promoter function of CEBPB that facilitated CRC cell proliferation by regulating multiple oncogenic pathways such as MAPK,PI3K-Akt,and Ras signaling.Next,by integrating a fine-mapping analysis and three independent case-control studies in Chinese populations consisting of 8,039 cases and 12,775 controls,we elucidated that rs1810503,a putative functional variant regulating CEBPB,was associated with CRC risk(OR=0.90,95%CI=0.86–0.93,P=1.07×10^(−7)).The association between rs1810503 and CRC risk was further validated in three additional multi-ancestry populations consisting of 24,254 cases and 58,741 controls.Mechanistically,the rs1810503 A to T allele change weakened the enhancer activity in an allele-specific manner to decrease CEBPB expression via longrange promoter-enhancer interactions,mediated by the transcription factor,REST,and thus decreased CRC risk.In summary,our study provides a genetic resource and a generalizable strategy for CRC etiology investigation,and highlights the biological implications of CEBPB in CRC tumorigenesis,shedding new light on the etiology of CRC.展开更多
基金supported by National Key Research and Development Program of China[2018YFD0900601]L.Chen,the open project fund from Laboratory for Marine Biology and Biotechnology,Qingdao National Laboratory for Marine Science(OF2019NO01)+1 种基金Doctor Fund of Shanghai Ocean University(A2-2006-21-200304)Science and Technology Development Fund of Shanghai Ocean University(A2-2006-20-200201)to W.Li.
文摘Epiboly,the coordinated spreading of the enveloping layer(EVL),the yolk syncytial layer(YSL)and the deep cells(DCs)toward the vegetal pole,is required for gastrulation.Interference with the EVL leads to early developmental failure.However,the genetic factors underlying EVL differentiation are so far unknown.By in-depth analyzing of single-cell sequencing data from 4 h post fertilization zebrafish embryos,we identified 105 genes(FDR<0.05)which showed highly specific EVL expression,among which the transcription factor cebpb and genes(krt18,cldne,cldnb,krt4,krt5)involved in cell-cell junction formation were exclusively expressed in EVL.To explore the role of cebpb in EVL differentiation,we knocked down its expression by morpholino-labeled antisense RNA.The morphant embryos showed disrupted EVL and developmental termination prior to epiboly.In accordance,expression of the EVL specific cell-adhesion molecule genes were significantly reduced.Thus,cebpb is the earliest EVL marker and essential for EVL differentiation in zebrafish.The elucidation of the specific EVL gene set provides us new insights into the molecular mechanisms underlying EVL differentiation.
基金This work was supported by the National Natural Science Foundation of China(82103929,82273713)Young Elite Scientists Sponsorship Program by CAST(2022QNRC001)+7 种基金Fundamental Research Funds for the Central Universities(WHU:2042022kf1205)Knowledge Innovation Program of Wuhan(whkxjsj011)Translational Medicine and Interdisciplinary Research Joint Fund of Zhongnan Hospital of Wuhan University(ZNJC202207)for Jianbo TianDistinguished Young Scholars of China(81925032)Key Program of National Natural Science Foundation of China(82130098)the Leading Talent Program of the Health Commission of Hubei Province,Natural Science Foundation of Hubei Province(2019CFA009)the Fundamental Research Funds for the Central Universities(2042022rc0026,2042023kf1005)for Xiaoping Miaothe National Natural Science Foundation of China(82204128)for Xiaoyang Wang.
文摘Genome-wide association studies(GWASs)have identified over 140 colorectal cancer(CRC)-associated loci;however,target genes at the majority of loci and underlying molecular mechanisms are poorly understood.Here,we utilized a Bayesian approach,integrative risk gene selector(iRIGS),to prioritize risk genes at CRC GWAS loci by integrating multi-omics data.As a result,a total of 105 high-confidence risk genes(HRGs)were identified,which exhibited strong gene dependencies for CRC and enrichment in the biological processes implicated in CRC.Among the 105 HRGs,CEBPB,located at the 20q13.13 locus,acted as a transcription factor playing critical roles in cancer.Our subsequent assays indicated the tumor promoter function of CEBPB that facilitated CRC cell proliferation by regulating multiple oncogenic pathways such as MAPK,PI3K-Akt,and Ras signaling.Next,by integrating a fine-mapping analysis and three independent case-control studies in Chinese populations consisting of 8,039 cases and 12,775 controls,we elucidated that rs1810503,a putative functional variant regulating CEBPB,was associated with CRC risk(OR=0.90,95%CI=0.86–0.93,P=1.07×10^(−7)).The association between rs1810503 and CRC risk was further validated in three additional multi-ancestry populations consisting of 24,254 cases and 58,741 controls.Mechanistically,the rs1810503 A to T allele change weakened the enhancer activity in an allele-specific manner to decrease CEBPB expression via longrange promoter-enhancer interactions,mediated by the transcription factor,REST,and thus decreased CRC risk.In summary,our study provides a genetic resource and a generalizable strategy for CRC etiology investigation,and highlights the biological implications of CEBPB in CRC tumorigenesis,shedding new light on the etiology of CRC.
