Current Status and Prospects of the Single-Cell Sequencing Technologies for Revealing the Pathogenesis of Pregnancy-Associated Disorders
Abstract
:1. Introduction
2. scRNA-seq: Laboratory Technologies and Bioinformatic Data Analysis Instruments
2.1. Laboratory Protocols
2.2. Data Analysis Methods in scRNA-seq
3. The Recent Discoveries in the scRNA-seq Studies of Human Pregnancy
3.1. Results of the scRNA-seq Studies of Normal Pregnancy Conditions
3.2. Results of the scRNA-seq Studies of Pregnancy Complications and Pregnancy-Associated Diseases
3.2.1. Hyperglycemia in Pregnancy
3.2.2. Preeclampsia
3.2.3. Preterm Labor
3.2.4. Recurrent Pregnancy Loss
3.2.5. Conditions Associated with an Increased Risk of Pregnancy Complications
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Year Ref. | Sample Type | Research Group | Gestational Age | Number of Cells | Method | Main Bioinformatic Tools * | Main Findings |
---|---|---|---|---|---|---|---|
Normal pregnancy | |||||||
2018 [60] | Placenta | Normal pregnancy (n = 8) | 8 and 24 weeks | 1567 | MACS, smart-seq2 | TopHat, HTSeq, Seurat, Monocle2, KEGG | Fourteen subtypes of placental cells: three CTBs1 subtypes, STBs2 subtype, EVTs3 subtypes, two macrophages’ cells subtypes, two mesenchymal stromal cells subtypes, one blood cell subtype in the villi, and two EVTs3 subtypes in the decidua. |
2018 [61] | Villi and decidua | Villi (n = 8), decidua (n = 6), | 6–11 weeks, elective termination | 21,095 | Cell counter, Drop-seq, 10X Genomics | STAR, featureCounts, Seurat, DAVID | Transcriptome definition of 20 cell populations; the relative proportions of each cell type in villi and decidual samples; an interactome map between the most abundantly expressed ligands and receptors in villi and decidua cells; the new subtypes of the FB4-like cells. |
2018 [21] | Placenta, decidua cells, maternal PBMC7 | Decidua (n = 11), placenta (n = 5), PBMC (n = 6) | 6–14 weeks | >70,000 | FACS, 10X Genomics, smartSeq2 | Cell Ranger, HISAT2, HTSeq, Seurat, Monocle2, Cytoscape, CellPhoneDB | Molecular and cellular map of the human decidual-placental interface; characterization of three DSC5 cell subtypes (dS1, dS2, and dS3) and three dNK6 subtypes; differentiation trajectory from CTB1 to EVT3; repository of ligand-receptor complexes to predict interactions between different cells of the maternal-fetal interface (CellPhoneDB). |
2022 [62] | Placenta | After delivery (n = 8), full-term | 38–40 weeks | 11,438 | MACS, 10X Genomics | Cell Ranger, Seurat, Monocle2, scanpy, clusterProfiler, CellPhoneDB | The maternal–fetal interface cellular map of full-term placenta; a subpopulation of TPLCs8 with high expression of HMMR; downregulation of PRDM6 may lead to an abnormal endovascular EVTs3 differentiation process in preeclampsia. |
2023 [63] | Villi | Normal pregnancy (n = 11), | 6–16 weeks, elective termination | 52,179 | HTBS9, 10X Genomics | Cell Ranger, Seurat, Monocle 2, CellPhoneDB | Three new populations of progenitor cells: endothelial progenitors, STB2 progenitors, and EVT3 progenitors; 8–9 gestational weeks were determined as a critical time point for altering gene expression profiles in placental cells. |
2022 [64] | Myometrium | Term in spontaneous labor (n = 11), term not in labor (n = 13), | ≥37 weeks, caesarean section | 53,194 | Cellometer Auto 2000; 10X Genomics | Cell Ranger, kallisto, bus tools, STAR, SingleR, Seurat, DESeq2, clusterProfiler, SPSS | A single-cell atlas of the human myometrium; cell–cell communications that are modulated during the physiologic process of spontaneous labor at term; ERRFI1, a specifically differentially expressed gene in maternally circulating monocytes; nonimmune and immune cells participate in a plethora of biological pathways associated with the contractile and inflammatory processes of spontaneous labor at term. |
2022 [65] | PBMC | Normal pregnancy (n = 131), non-pregnancy (n = 5) | 6–40 weeks | 198,356 | HTBS9, MGI DNBelab, TF Scientific | PISA, Seurat, clusterProfiler, CellChat, MAGIC algorithm, SHAP | A single-cell atlas of PBMCs7 in pregnant women spanning the entire gestation period; cell-type-specific model to predict gestational age in normal pregnancy; interferon-stimulated gene upregulation. |
2022 [66] | UCB10 cells | Normal (n = 4) | 31–37 weeks, after delivery | 3866 | Countess II, 10X Genomics | Cell Ranger | New cell types (erythroid cell, T cell, B cell, erythroid precursor cells, NK cell, and endothelial progenitor cell), new subpopulations (six different clusters of erythroid cells) in UCB10; the differentially expressed genes and chromatin accessibility in each cell between different gestational weeks. |
2022 [67] | UCB10 cells | Normal (n = 3) | After delivery | 57,467 | DNBelab C | STAR, PISA, Seurat, UMAP, bap2, clusterProfiler | Differential gene expression regulation between neonatal and adult T and B cells; the global molecular features of transcription and chromatin accessibility in neonatal UCB10 nucleated cells and adult PBMCs7. |
Gestational diabetes mellitus | |||||||
2021 [68] | Placenta | Gestational diabetes mellitus (n = 20), normal (n = 20) | Full-term, caesarean section | 27,220 | HTBS9, 10X Genomics | Cell Ranger, Seurat, SingleR, Monocle2, SCENIC, CellPhoneDB, Velocyto, GSVA | The comprehensive cell atlas for the gestational diabetes mellitus placenta; characterization of nine cell types in the human placenta; a significant increase of NK and cytotoxic T cells, enhancement of M2 macrophages, and decrease of inflammatory response cells in the gestational diabetes mellitus placenta; ligand-receptor interactions in the maternal and fetal microenvironment, as well as new marker genes, including SLC1A2, SLC1A6, ADRB1. |
Preeclampsia | |||||||
2017 [69] | Placenta | Early-onset preeclampsia (n = 4), normal (n = 6) | 28–32 weeks, healthy 38 weeks, cesarean section | >24,000 | 10X Genomics | Cell Ranger, STAR, Rtsne | A large-scale single-cell transcriptomic atlas of the normal and early preeclamptic placentas; the differentiation relationships between the CTBs1, STBs2, and EVTs3 were re-confirmed; a significant increase of variability and levels expression of cell death-related genes in early preeclamptic EVTs3; plasma cell-free RNAs may be useful as markers of placenta cellular composition and preeclampsia. |
2021 [70] | Placenta | Preeclampsia (n = 3), normal (n = 3) | 34–38 weeks, cesarean section | 11,518 | Singlerone GEXSCOPE | Ensembl, fastp, featureCounts, Seurat, clusterProfiler, Monocle 2, DDRTree | Differences in transcriptional profiles of STBs2, EVTs3, and VCTs11 between preeclampsia and healthy patients; VCTs11 and EVTs3 show immune response in preeclampsia; signaling pathways in STBs2 upregulated in the preeclampsia; three new VCTs11 subtypes; a significant increase of VCT-2 cells in the preeclampsia placenta. |
2022 [71] | Placenta | Early-onset preeclampsia (n = 2), healthy (n = 2) | 32–40 weeks, cesarean section | 29,008 | HTBS9, 10X Genomics | Cell Ranger, Seurat, SCENIC, scFunctions, GSEA, Cytoscape | Differences in transcriptional profiles of STBs2, EVTs3, and VCTs11 between preeclampsia and healthy patients; two new transcriptional factors, CEBPB and GTF2B, involved in EVTs3 dysfunction in preeclampsia. |
Recurrent pregnancy loss | |||||||
2021 [72] | Decidua | Recurrent pregnancy loss (n = 9), healthy (n = 15) | 7–9 weeks | 18,646 | FACS; 10X Genomics | Cell Ranger, Seurat, SAVER, velocyto, CellPhoneDB, Cytoscape | Changes in the number of dNK6 cells and macrophages function between recurrent pregnancy loss and normal pregnancy; a decrease of macrophage populations in recurrent pregnancy loss; a significant decrease of dNK6 subset with growth-supporting activity and an increase of pro-inflammatory dNK6 subset that produces cytokines in recurrent pregnancy loss; ligand/receptor level hypothesis about the likely causes underlying pregnancy failure. |
2021 [73] | PBMC7 decidua | Recurrent miscarriage (n = 14), normal (n = 10) | 6–8 weeks, therapeutic termination | 56,758 | 10X Genomics | Cell Ranger, Seurat | A comprehensive cellular and molecular atlas of decidual and peripheral leukocytes in early pregnancy; an increase of dNK3 subset with cytotoxic and immune-active; the unique accumulation of the dNK4 subset with pro-inflammatory properties in the recurrent miscarriages; increased expression of inflammation-related genes in dNK6 cells from recurrent miscarriages; cytotoxic properties of T cells, NK-cells, and mucosal-associated invariant T cells in peripheral blood. |
2021 [74] | Decidua | Recurrent spontaneous abortion (n = 6), normal (n = 5) | 5–8 weeks | 66,078 | 10X Genomics | Cell Ranger, STAR, Seurat, Monocle 2, CellPhoneDB, CellChat, SCENIC | Characterization of the five clusters of DSCs5; changes in the number of decidualized stromal cells in recurrent spontaneous abortion; cell composition and communications in normal and recurrent spontaneous abortion decidua at early pregnancy; the aberrant decidualization and obstructed communication between stromal cells accompanying recurrent spontaneous abortion. |
Preterm labor | |||||||
2019 [75] | Placenta | Preterm labor (n = 3), term no labor (n = 3), term in labor (n = 3), | Preterm (33–35 weeks), term labor (38–40 weeks) | 79,906 | Cellometer Auto 2000; 10X Genomics | Cell Ranger, STAR, Seurat, xCell, DESeq2 | Two cell types: lymphatic endothelial decidual cells in the chorioamniotic membranes and non-proliferative interstitial cytotrophoblasts in the placental villi; a significant increase of NFKB1 gene in macrophages from women with preterm labor. |
Conditions associated with an increased risk of pregnancy complications | |||||||
2016 [76] | Cumulus- oocyte complex | Polycystic ovary syndrome (n = 9), healthy (n = 7) | - | 28 cumulus cells | Smart-seq2 | Read alignment and quantification methods not disclosed; DAVID | Differentially expressed genes, including PPP2R1A, PDGFRA, EGFR, PTGS, CAV1, INHBB, etc., detected as potential causes of PCOS oocytes and CCs disorder at early stages; restoration of their normal expression level via assisted reproductive techniques, which can be an effective treatment for subfertile patients with PCOS. |
2020 [77] | Cumulus- oocyte complex | Polycystic ovary syndrome (n = 9), healthy (n = 7) | - | 28 cumulus cells | Smart-seq2 | Read alignment and quantification methods not disclosed; DAVID, DESeq2, WGCNA, Cytoscape, GSEA, clusterProfiler, | Downregulation of CYP26A1, MTRNR2L1, and ELOA genes, upregulation of FAM53A, PPP1R35, and BLM in PCOS oocytes; potential premature activation of mitochondrial function in PCOS oocytes. |
2020 [78] | Placenta | Healthy patients (n = 8) | 8–24 weeks | 1567 | MACS, smart-seq2 | TopHat, HTSeq, Seurat, Monocle2, ARACNe-AP, KEGG | ACE2 expression in EVTs3 of the first and second trimester placenta; BSG/CD147, the alternate receptor for SARS-CoV-2, expressed by almost all the placental cells; an abundant expression of DPP4 (MERS-CoV receptor) and ANPEP (CoV-229E receptor) in the cells of the placenta; co-expression of BSG/CD147 with ACE2 in STBs2 and EVTs3; an increased incidence of preterm delivery in women with COVID-19 was assumed. |
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Naydenov, D.D.; Vashukova, E.S.; Barbitoff, Y.A.; Nasykhova, Y.A.; Glotov, A.S. Current Status and Prospects of the Single-Cell Sequencing Technologies for Revealing the Pathogenesis of Pregnancy-Associated Disorders. Genes 2023, 14, 756. https://doi.org/10.3390/genes14030756
Naydenov DD, Vashukova ES, Barbitoff YA, Nasykhova YA, Glotov AS. Current Status and Prospects of the Single-Cell Sequencing Technologies for Revealing the Pathogenesis of Pregnancy-Associated Disorders. Genes. 2023; 14(3):756. https://doi.org/10.3390/genes14030756
Chicago/Turabian StyleNaydenov, Dmitry D., Elena S. Vashukova, Yury A. Barbitoff, Yulia A. Nasykhova, and Andrey S. Glotov. 2023. "Current Status and Prospects of the Single-Cell Sequencing Technologies for Revealing the Pathogenesis of Pregnancy-Associated Disorders" Genes 14, no. 3: 756. https://doi.org/10.3390/genes14030756
APA StyleNaydenov, D. D., Vashukova, E. S., Barbitoff, Y. A., Nasykhova, Y. A., & Glotov, A. S. (2023). Current Status and Prospects of the Single-Cell Sequencing Technologies for Revealing the Pathogenesis of Pregnancy-Associated Disorders. Genes, 14(3), 756. https://doi.org/10.3390/genes14030756