Single Cell Genomics

About the Program

The Perinatal Single-Cell Genomics Unit implements the latest state-of-the-art microfluidic technological advances to study the placenta and other reproductive tissues during pregnancy at single-cell resolution. To analyze and integrate the data, we develop and utilize innovative computational and statistical tools to gain a deeper knowledge of the molecular underpinning of the fetal-maternal dialog at single-cell resolution. Our aim is to identify biomarkers for early prediction of major obstetrical syndromes and to identify target genes that may open new avenues for treatment with precision medicine.


  • To implement microfluidic technology to study the placenta and other reproductive tissues at single-cell resolution.
  • To characterize the cell-type composition of different placental compartments and the molecular underpinnings of the maternal-fetal dialog during pregnancy.
  • To develop novel computational tools and statistical models to analyze the gene expression signatures and the epigenomic profiles of placental tissues obtained from pregnancies with and without obstetrical complications.
  • In collaboration with the other units (Bioinformatics, Immunology, Microbiology) of the Perinatology Research Branch, to generate a comprehensive longitudinal multi-omics characterization of human pregnancy to develop better biomarkers and to facilitate early detection of the major obstetrical syndromes.
  • To study the effects of genetic variants on molecular phenotypes and to use Mendelian randomization and mediation analysis to dissect the causal pathway between altered gene expression and pregnancy-related phenotypes

Research Focus

  • Cell-types that define the different placental tissues during pregnancy.
  • How these genes are expressed during gestation for different cell-types.
  • The spatial distribution of the maternal and fetal cellular composition of the human placenta.
  • The interaction of maternal and fetal immune cells at the molecular level.
  • The Identification of genes and cell-types involved in the molecular mechanisms leading to a specific obstetrical syndrome (preterm birth, preeclampsia, fetal death, and more).
  • The identification of molecular mechanisms and genetic pathways that underlie genetic variants associated with pregnancy related phenotypes.


  • Characterized the molecular common pathway of labor and term and preterm parturition at single-cell resolution.
  • Determined that co-expression of the ACE2 and TMPRSS2 transcripts is negligible in the placenta and chorioamniotic membranes. This finding indicates why SARS-CoV-2 is rarely vertically transmitted.

Selected Publications

  • Pique-Regi R, Romero R, Tarca AL, Luca F, Xu Y, Alazizi A, Leng Y, Hsu CD, Gomez-Lopez N. Does the human placenta express the canonical cell entry mediators for SARS-CoV-2? Elife. 2020 Jul 14; 9:e58716. PMID: 32662421
  • Tarca AL, Romero R, Pique-Regi R, Pacora P, Done B, Kacerovsky M, Bhatti G, Jaiman S, Hassan SS, Hsu CD, Gomez-Lopez N. Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy. BMC Med Genomics. 2020 Feb 12; 13:25. PMID: 32050959
  • Pique-Regi R, Romero R, Tarca AL, Sendler ED, Xu Y, Garcia-Flores V, Leng Y, Luca F, Hassan SS, Gomez-Lopez N. Single cell transcriptional signatures of the human placenta in term and preterm parturition. Elife. 2019 Dec 12; 8:e52004. PMID: 31829938

Distinguished Faculty


Roger Pique-Regi, PhD

Associate Professor, Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University School of Medicine