Demonstration of RNA Sequencing of Circulating Trophoblast Cells from Maternal Blood

During pregnancy, rare trophoblast cells from the placenta circulate in maternal blood and could offer a liquid-biopsy view of placental function; this Society of Reproductive Investigation 2024 poster demonstrates a proof-of-concept RareCyte workflow that isolates individual circulating trophoblasts from a maternal blood sample and profiles them by single-cell RNA sequencing.

Presented by RareCyte and Swedish Medical Center.

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• The workflow isolates individual circulating trophoblast cells from a 40 mL maternal blood draw and prepares each one for single-cell RNA sequencing. Nucleated cells are concentrated with the AccuCyte system, trophoblasts are enriched immunomagnetically and imaged on the CyteFinder instrument, and single cells are then retrieved with the CytePicker module, deposited individually into tubes, and sequenced to an average depth of about 50 million reads.
• Forty-eight pregnant participants were enrolled at a median gestational age of 33 weeks, and 48 circulating trophoblast cells met the study's criteria for molecular certification, with 8 additional cells classified as trophoblast-white blood cell hybrids. Gestational age ranged from 25 to 40 weeks; each cell was certified against a curated panel of 36 literature-derived trophoblast markers scored alongside canonical white blood cell markers, and an average of about 6,500 protein-coding genes were detected per cell, ranging from roughly 3,000 to 17,000.
• As a proof of concept, the single-cell transcriptomes separated trophoblasts from white blood cells and produced a distinct trophoblast gene-expression signature. Comparing the top 29 certified trophoblast cells against two live white blood cells sequenced in parallel identified 109 differentially expressed genes at an adjusted p-value below 1E-03, including the cytokeratin genes KRT8, KRT18 and KRT19, and principal-component analysis clustered the trophoblasts apart from the white blood cells; the authors frame the result as a third-trimester proof of concept rather than a validated clinical test.