The Prediction Of Gene Expression Profile Based On Maternal Plasma CfDNA Nucleosome Footprint In Aneuploid And Healthy Term Pregnancy

BackgroundGene expression profiling studies are now used to predict prognosis and guide the treatment protocols of various diseases.In pregnancy,research on fetal and placental gene expression profiling during pregnancy has been slow due to ethical and abortion risk factors involved in sampling fetal samples.The nucleosome footprint of cell-free DNA(cfDNA)carries information on the gene expression profile of the original tissues and thus may be used to predict the physiological and pathological status of the individual.The plasma cfDNA of pregnant women is mainly derived from maternal immune cells and placental trophoblast cells,so it may theoretically be used to predict gene expression information in the placenta and maternal immunity during pregnancy.Because plasma samples can be taken multiple times,it is possible to use plasma cfDNA to study gene expression profiles during placental development.However,its feasibility is yet to be supported by the data.Aneuploid pregnancies are characterized by abnormal development and early abortion,and the association analysis between abnormal phenotypes and expression profiles can be used to verify the feasibility of plasma cfDNA to predict the gene expression profiles of the placenta and maternal immune cells in abnormal pregnancies.Due to the limitation of sampling,there are few data related to placental gene expression profiles during gestational development.This study will attempt to establish the gene expression profiles of the placenta and maternal immune cells in different gestational periods.Based on the study that promoter fragmentation patterns in cfDNA can reflect its tissue cell origin and can predict gene expression,this study is intended to verify the feasibility of monitoring gene expression profiles by comparing the correlation between cfDNA nucleosome distribution patterns and phenotypic characteristics in aneuploid pregnancies,and to study the dynamic changes in placental gene expression profiles during pregnancy through cfDNA nucleosome distribution patterns at different gestational periods,providing a research idea for non-invasive detection of physiological and pathological states during pregnancy.MethodsIn this study,we performed whole-genome sequencing of plasma cfDNA based on non-invasive prenatal testing(NIPT)screening of pregnant women carrying a fetus with trisomy and healthy pregnant women of different gestations,and analyzed gene expression by identifying differential genes according to the cfDNA nucleosome profile in the region around the transcription start sites(TSSs).The differentially expressed genes were then further analyzed by GO and KEGG functional enrichment analysis to determine their biological roles.1.To assess the degree of association between predicted gene expression profiles based on cfDNA nucleosome distribution patterns and abnormal pregnancy phenotypic characteristics in a sample of 101 pregnant women with aneuploid pregnancy(trisomy 21,18,13)by combining literature.2.To collect plasma samples from 150 pregnant women with healthy pregnancy at different trimesters(early,mid:mid 1,mid 2,mid 3,late)and non-pregnant women.Gene expression profiles inferred based on cfDNA nucleosome distribution patterns were assessed in comparison with physiological changes in pregnancy by combining literature.Results1.In aneuploid abnormal pregnancy,we identified genes with different trisomy pregnancy-associated expression patterns,and differential gene enrichment results were strongly associated with common or unique genetic phenotypes of trisomic fetuses(mental retardation,impaired growth,and multiple malformations).It was also associated with several pathways that play an important role in embryonic development(e.g.,MAPK,Hippo,TGF-β,and Rap1 signaling pathways).Immune-related differential genes were mainly associated with the maintenance of embryonic homeostasis and normal development.2.In this longitudinal analysis of healthy term pregnancy,we also identified gene expression changes that support the differences in fetal development regulation and immune system function during pregnancy.Functional enrichment and signaling pathway analysis revealed that differential genes are mainly enriched in the pathway of transcription and translation of genetic material,metabolism of organic compounds,and including immune regulation.We also identified differentially expressed genes with significant temporal trends during pregnancy progression.Genes with an overall trend towards up-regulation were mainly associated with development,while the down-regulation genes were mainly related to immune system responses.Reflecting the adaptation of the placenta and mother to different environments with the development of pregnancy.ConclusionThe feasibility and application value of the method was preliminarily demonstrated by comparing the correlation between the gene expression profiles inferred from the cfDNA nucleosome distribution patterns in plasma of aneuploid pregnant women and the phenotypic characteristics of chromosome aneuploid pregnancy.Subsequently,the feasibility of this non-invasive method was again demonstrated by characterizing differential genetic changes in pregnancy progression,which may also provide research ideas for the non-invasive detection of physiological and pathological states in other diseases.