目的筛选和验证潜在的调控特发性肺纤维化(IPF)发生发展的基因,为IPF治疗提供新的靶点。方法通过使用转化生长因子β_(1)(TGF-β_(1))处理HFL1细胞诱导体外IPF模型(TGF-β_(1)处理组),同时以未处理细胞作为空白对照组,提取细胞RNA并进...目的筛选和验证潜在的调控特发性肺纤维化(IPF)发生发展的基因,为IPF治疗提供新的靶点。方法通过使用转化生长因子β_(1)(TGF-β_(1))处理HFL1细胞诱导体外IPF模型(TGF-β_(1)处理组),同时以未处理细胞作为空白对照组,提取细胞RNA并进行转录组测序。对转录组测序结果进行分析,筛选处理组与对照组间的差异表达基因。同时,进行了Gene Ontology(GO)、Kyoto Encyclopedia of Genes and Genomes(KEGG)和Gene Set Enrichment Analysis(GSEA)功能富集分析。使用IPF疾病相关的GEO数据集GSE24206和GSE40839结合转录组测序数据筛选出关键基因。通过IPF体外模型的RTq PCR实验对这些关键基因进行验证,并筛选出核心基因。最后通过腹腔注射博来霉素构建小鼠IPF模型,通过RT-qPCR对等渗盐水对照组和博来霉素处理组样本进行检测,验证筛选出的核心基因表达变化。结果相较于空白对照组,TGF-β_(1)处理组中α-SMA、NOX4和PDGFA 3种因子的表达均显著上调,表明体外IPF诱导模型构建成功。转录组测序分析筛选出2345个差异表达基因。差异基因的GO和KEGG富集分析显示,显著富集的通路包括TGF-β响应及TGF-β信号通路等;GSEA分析则富集到RNA降解、氧化磷酸化等通路。通过GEO数据库和转录组测序数据相交筛选出26个与IPF密切相关的基因。经验证,确定SLC19A2和IFI44为影响IPF的核心基因。在小鼠IPF模型中,相较于等渗盐水对照组,博来霉素处理组肺组织中SLC19A2显著上调,IFI44显著下调,这与IPF体外模型中的结果相一致。结论SLC19A2基因和IFI44基因可能是治疗IPF疾病的新靶点,这为IPF的研究和治疗提供了新思路。展开更多
Importance: The current lack of reliable rapid tests for distinguishing between bacterial and viral infections has contributed to antibiotic misuse.Objective: This study aimed to develop a novel biomarker assay that i...Importance: The current lack of reliable rapid tests for distinguishing between bacterial and viral infections has contributed to antibiotic misuse.Objective: This study aimed to develop a novel biomarker assay that integratesFAM89A andIFI44L measurements to assist in differentiating between bacterial and viral infections.Methods: This prospective study recruited children with febrile illness from two hospitals between July 1, 2018, and June 30, 2019. A panel of three experienced pediatricians performed reference standard diagnoses of all patients (i.e., bacterial or viral infection) using available clinical and laboratory data, including a 28-day follow-up assessment. Assay operators were blinded to the reference standard diagnoses. The expression levels ofFAM89A andIFI44L were determined by quantitative real-time polymerase chain reaction assessment.Results: Of 133 potentially eligible patients with suspected bacterial or viral infection, 35 were excluded after the application of exclusion criteria. The resulting cohort included 98 patients: 59 with viral diagnoses and 39 with bacterial diagnoses. The areas under the curve (AUCs) of diagnoses usingFAM89A andIFI44L were 0.694 [95% confidence interval (CI): 0.583-0.804] and 0.751 (95%CI: 0.651-0.851), respectively. The disease risk score (DRS) [log2(FAM89A expression) - log2(IFI44L expression)] signature achieved an improved area under the receiver operating characteristic curve (AUC, 0.825;95%CI: 0.735-0.915), compared with the AUC generated from individual host RNA. A combination of the DRS and the C-reactive protein (CRP) level achieved an AUC of 0.896 (95%CI: 0.825-0.966). Optimal cutoffs for the DRS and CRP level were -3.18 and 19.80 mg/L, respectively.Interpretation: The DRS was significantly more accurate than the CRP level in distinguishing between bacterial and viral infections;the combination of these two parameters exhibited greater sensitivity and specificity. This study provides information that could be useful for the clinical application ofFAM89A andIFI44L in terms of distinguishing between viral and bacterial infections.展开更多
The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying pheno...The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, Chinese indigenous breeds,African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group,while the Chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including IFI44 and IFI44L genes and PANK2 and RNF24 genes, associated with immune response and visual function.Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation,energy metabolism, and growth development.Furthermore, the IFI44 and IFI44L genes showed a common selection signature in the genomes of 30domesticated sheep breeds. The IFI44 c. 54413058C>G mutation was selected for genotyping and population genetic validation. Results showed that the IFI44 polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.展开更多
文摘目的筛选和验证潜在的调控特发性肺纤维化(IPF)发生发展的基因,为IPF治疗提供新的靶点。方法通过使用转化生长因子β_(1)(TGF-β_(1))处理HFL1细胞诱导体外IPF模型(TGF-β_(1)处理组),同时以未处理细胞作为空白对照组,提取细胞RNA并进行转录组测序。对转录组测序结果进行分析,筛选处理组与对照组间的差异表达基因。同时,进行了Gene Ontology(GO)、Kyoto Encyclopedia of Genes and Genomes(KEGG)和Gene Set Enrichment Analysis(GSEA)功能富集分析。使用IPF疾病相关的GEO数据集GSE24206和GSE40839结合转录组测序数据筛选出关键基因。通过IPF体外模型的RTq PCR实验对这些关键基因进行验证,并筛选出核心基因。最后通过腹腔注射博来霉素构建小鼠IPF模型,通过RT-qPCR对等渗盐水对照组和博来霉素处理组样本进行检测,验证筛选出的核心基因表达变化。结果相较于空白对照组,TGF-β_(1)处理组中α-SMA、NOX4和PDGFA 3种因子的表达均显著上调,表明体外IPF诱导模型构建成功。转录组测序分析筛选出2345个差异表达基因。差异基因的GO和KEGG富集分析显示,显著富集的通路包括TGF-β响应及TGF-β信号通路等;GSEA分析则富集到RNA降解、氧化磷酸化等通路。通过GEO数据库和转录组测序数据相交筛选出26个与IPF密切相关的基因。经验证,确定SLC19A2和IFI44为影响IPF的核心基因。在小鼠IPF模型中,相较于等渗盐水对照组,博来霉素处理组肺组织中SLC19A2显著上调,IFI44显著下调,这与IPF体外模型中的结果相一致。结论SLC19A2基因和IFI44基因可能是治疗IPF疾病的新靶点,这为IPF的研究和治疗提供了新思路。
基金This study was supported by the Special Fund of the National Science and Technology Major Project of China(No. 2018ZX10305409)Beijing Hospital Authority "Dengfeng" Talent Training Plan(DFL 20181201)Sanming Project of Medicine in Shenzhen(SZSM201512030)
文摘Importance: The current lack of reliable rapid tests for distinguishing between bacterial and viral infections has contributed to antibiotic misuse.Objective: This study aimed to develop a novel biomarker assay that integratesFAM89A andIFI44L measurements to assist in differentiating between bacterial and viral infections.Methods: This prospective study recruited children with febrile illness from two hospitals between July 1, 2018, and June 30, 2019. A panel of three experienced pediatricians performed reference standard diagnoses of all patients (i.e., bacterial or viral infection) using available clinical and laboratory data, including a 28-day follow-up assessment. Assay operators were blinded to the reference standard diagnoses. The expression levels ofFAM89A andIFI44L were determined by quantitative real-time polymerase chain reaction assessment.Results: Of 133 potentially eligible patients with suspected bacterial or viral infection, 35 were excluded after the application of exclusion criteria. The resulting cohort included 98 patients: 59 with viral diagnoses and 39 with bacterial diagnoses. The areas under the curve (AUCs) of diagnoses usingFAM89A andIFI44L were 0.694 [95% confidence interval (CI): 0.583-0.804] and 0.751 (95%CI: 0.651-0.851), respectively. The disease risk score (DRS) [log2(FAM89A expression) - log2(IFI44L expression)] signature achieved an improved area under the receiver operating characteristic curve (AUC, 0.825;95%CI: 0.735-0.915), compared with the AUC generated from individual host RNA. A combination of the DRS and the C-reactive protein (CRP) level achieved an AUC of 0.896 (95%CI: 0.825-0.966). Optimal cutoffs for the DRS and CRP level were -3.18 and 19.80 mg/L, respectively.Interpretation: The DRS was significantly more accurate than the CRP level in distinguishing between bacterial and viral infections;the combination of these two parameters exhibited greater sensitivity and specificity. This study provides information that could be useful for the clinical application ofFAM89A andIFI44L in terms of distinguishing between viral and bacterial infections.
基金supported by the National Key R&D Program of China (2021YFD1300901)National Natural Science Foundation of China (31960653)+1 种基金West Light Foundation of the Chinese Academy of SciencesNational Joint Research on Improved Breeds of Livestock and Poultry (19210365)。
文摘The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, Chinese indigenous breeds,African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group,while the Chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including IFI44 and IFI44L genes and PANK2 and RNF24 genes, associated with immune response and visual function.Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation,energy metabolism, and growth development.Furthermore, the IFI44 and IFI44L genes showed a common selection signature in the genomes of 30domesticated sheep breeds. The IFI44 c. 54413058C>G mutation was selected for genotyping and population genetic validation. Results showed that the IFI44 polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.
