Differential gene expression during placentation in pregnancies conceived with different fertility treatments compared with spontaneous pregnancies

This SMAART cohort study uses bulk total RNA-sequencing to assses the impact of mode of conception on first trimester human placenta gene expression [PMID: 30611556]. Pregnancies were singleton, gestational age 10-14 weeks, normal karyotype, fetal race Caucasian or biracial Caucasian/Asian, and conceived either with fertility treatments (IVF=in vitro fertilization, NIFT=non-IVF fertility treatment) or without fertility treatments (spontaneous, also called unassisted). Pregnancies were balanced for fetal sex. Chorionic villi tissue leftover after clinical genetic testing was collected for research with informed consent and stored in RNAlater RNA Stabilization Reagent (QIAGEN) at -80C until RNA isolation with the AllPrep DNA/RNA Mini Kit (QIAGEN). RNA-seq libraries of >200 nt were constructed with Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina) and depleted of cytoplasmic and mitochondrial ribosomal RNAs. After quality check with FastQC, transcript abundances were quantified against the human reference genome (Ensembl build GRCh38) using Kallisto. Differential expression analysis with DESeq2 was performed to compare mode of conception, adjusted for fetal sex and RNA-seq dataset. The dataset adjustment corrected for batch effects from RNA isolation and/or sequencing runs. There were N=141 subjects total, including 74 spontaneous, 33 non-IVF (NIFT), and 34 IVF pregnancies. The subject columns at the end of the DESeq2 files are counts normalized for sequencing depth. Overall design: Total RNA-seq differential gene expression analysis comparing different modes of conception: infertility treatments (IVF and NIFT together) vs spontaneous, NIFT vs spontaneous, IVF vs spontaneous, and IVF vs NIFT. Analysis was adjusted for fetal sex and RNA-seq dataset in the DESeq2 model.