Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

Kolodziejczyk, Aleksandra A.; Kim, Jong; Tsang, Jason C.H.; Ilicic, Tomislav; Henriksson, Johan; Natarajan, Kedar Nath; Tuck, Alex; Gao, Xuefei; Bühler, Marc; Liu, Pentao; Marioni, John C.; Teichmann, Sarah A.

doi:10.1016/j.stem.2015.09.011

Cited by 526 publications

(584 citation statements)

References 72 publications

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“…S4B). As geneexpression heterogeneity decreased with increasing expression levels (49,50) (Fig. S4C), we quantified the expression heterogeneity of each gene as the vertical distance of its squared coefficient of variations (CV 2 ) from the median CV 2 [distance to median (DM)] at its corresponding expression level in a double log-transformed space (50).…”

Section: Deciphering Cellular Aberrations In Preeclamptic Placentas Frommentioning

confidence: 99%

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Tsang

Vong

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

258

267

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The human placenta is a dynamic and heterogeneous organ critical in the establishment of the fetomaternal interface and the maintenance of gestational well-being. It is also the major source of cell-free fetal nucleic acids in the maternal circulation. Placental dysfunction contributes to significant complications, such as preeclampsia, a potentially lethal hypertensive disorder during pregnancy. Previous studies have identified significant changes in the expression profiles of preeclamptic placentas using whole-tissue analysis. Moreover, studies have shown increased levels of targeted RNA transcripts, overall and placental contributions in maternal cell-free nucleic acids during pregnancy progression and gestational complications, but it remains infeasible to noninvasively delineate placental cellular dynamics and dysfunction at the cellular level using maternal cell-free nucleic acid analysis. In this study, we addressed this issue by first dissecting the cellular heterogeneity of the human placenta and defined individual cell-type-specific gene signatures by analyzing more than 24,000 nonmarker selected cells from full-term and early preeclamptic placentas using large-scale microfluidic single-cell transcriptomic technology. Our dataset identified diverse cellular subtypes in the human placenta and enabled reconstruction of the trophoblast differentiation trajectory. Through integrative analysis with maternal plasma cell-free RNA, we resolved the longitudinal cellular dynamics of hematopoietic and placental cells in pregnancy progression. Furthermore, we were able to noninvasively uncover the cellular dysfunction of extravillous trophoblasts in early preeclamptic placentas. Our work showed the potential of integrating transcriptomic information derived from single cells into the interpretation of cell-free plasma RNA, enabling the noninvasive elucidation of cellular dynamics in complex pathological conditions. single-cell transcriptomics | cell-free RNA | noninvasive prenatal testing | placenta | preeclampsia

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Section: Deciphering Cellular Aberrations In Preeclamptic Placentas Frommentioning

confidence: 99%

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Tsang

Vong

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

258

267

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“…S2B). The possible differences in heterogeneity of gene expression in terms of functional categories between Dnmt3a WT/WT and Dnmt3a R878H/WT mice were further investigated (Dataset S3): We compared distance-to-the-median (DM) values of genes in mouse pairs for each Gene Ontology (GO term) as previously described (17). Altogether, 1,039 GO terms revealed significant differences in at least one pairwise comparison (P < 0.01) (Dataset S4).…”

Section: Single-cell Transcriptome Profiling Of Lsks In Dnmt3a R878h/mentioning

confidence: 99%

Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement

Dai

Wang

Huang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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DNMT3A is frequently mutated in acute myeloid leukemia (AML). To explore the features of human AML with the hotspot DNMT3A R882H mutation, we generated Dnmt3a R878H conditional knockin mice, which developed AML with enlarged Lin − Sca1 + cKit + cell compartments. The transcriptome and DNA methylation profiling of bulk leukemic cells and the single-cell RNA sequencing of leukemic stem/progenitor cells revealed significant changes in gene expression and epigenetic regulatory patterns that cause differentiation arrest and growth advantage. Consistent with leukemic cell accumulation in G 2 /M phase, CDK1 was up-regulated due to mTOR activation associated with DNA hypomethylation. Overexpressed CDK1-mediated EZH2 phosphorylation resulted in an abnormal trimethylation of H3K27 profile. The mTOR inhibitor rapamycin elicited a significant therapeutic response in Dnmt3a R878H/WT mice.have been identified in a subset of acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and acute lymphoblastic leukemia (ALL), with DNMT3A R882 being the hotspot (1-4). Clinical features of most AML cases with DNMT3A mutations include preferential involvement of a monocytic lineage (AML-M4 and -M5 subtypes), thrombocytosis, onset at a relatively old age, and poor prognosis (2, 5, 6). Careful genotypephenotype correlations suggest that patients manifest DNMT3A mutations in preleukemic hematopoietic stem cells (HSCs)/multipotent progenitors (MPPs), which exhibit a competitive advantage over normal HSCs. Because these mutations occur at a very early stage among genetic abnormalities, they are likely involved in the development of leukemia (7,8).Functionally, the DNMT3A R882 mutation might disrupt epigenetic regulation. This kind of DNMT3A mutation confers reduced methyltransferase activity and promotes the possibility of dominant-negative consequences compared with the wild-type (WT) allele (2, 9, 10). Moreover, the DNMT3A mutation causes aberrant DNA hypomethylation and up-regulates a series of target genes involved in AML pathogenesis (11-13).In vivo animal tests have shown that the Dnmt3a gene plays an essential role in hematopoiesis regulation. Dnmt3a −/− HSCs expand remarkably, but their differentiation is inhibited when Dnmt3a is conditionally inactivated in the murine hematopoietic system; this phenomenon is consistent with a preleukemic state (7). Moreover, all lethally irradiated mice transplanted with Dnmt3a-deleted HSCs died within 1 y and were diagnosed with a spectrum of malignancies similar to those observed in patients carrying DNMT3A mutations, including MDS, AML, primary myelofibrosis, and ALL, suggesting that Dnmt3a functions as a tumor suppressor (7). With a second hit of mutations in various genes such as N-RAS, C-KIT, or FLT3 in Dnmt3a −/− mice, Dnmt3a deletion induces leukemic transformation (14, 15). Although these results indicate a major role of Dnmt3a deletion in facilitating the development of leukemia, the in vivo roles of DNMT3A mutants in leukemogenesis still need to be addressed. In our previous work, b...

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“…A recently developed technique of single-cell RNA sequencing (scRNA-Seq) and single-cell highthroughput quantitative RT-PCR (qRT-PCR) provide opportunities to address these fundamental questions at a high resolution. Thus far, the single-cell techniques have been used to reveal pluripotency state transition and lineage segregation of embryonic stem cells and distinct cell types of preimplantation embryos (2)(3)(4)(5)(22)(23)(24)(25)(26). More recently, the technology was also used to decipher the mesodermal lineage diversification toward the hematopoietic system in the post-implantation embryo (27,28), and to compare the pluripotency state between preimplantation and post-implantation embryos (5,29).…”

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confidence: 99%

Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos

Wen

Zeng

Fang

et al. 2017

Journal of Biological Chemistry

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Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

Cited by 526 publications

References 72 publications

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement

Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos

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