StemMapper: a curated gene expression database for stem cell lineage analysis

Pinto, José; Machado, Rui S. R.; Magno, Ramiro; Oliveira, Daniel V.; Machado, Susana; Andrade, Raquel P.; Bragança, José; Duarte, Isabel Margarida; Futschik, Matthias E.

doi:10.1093/nar/gkx921

Cited by 28 publications

(19 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After reviewing almost all cancer single-cell sequencing studies, we concluded 14 crucial functional states of cancer cells, including stemness, invasion, metastasis, proliferation, EMT, angiogenesis, apoptosis, cell cycle, differentiation, DNA damage, DNA repair, hypoxia, inflammation and quiescence. To characterize these functional states for cancer single cells, we built the corresponding gene signatures through searching literatures and known databases (including some general databases, such as Gene Ontology (17) and MSigDB (18), and some specialized databases, such as Cyclebase (19), HCMDB (20) and StemMapper (21)) (Supplementary Table S2). For most of the signatures, the collected genes that were mentioned in more than two resources were kept.…”

Section: Methodsmentioning

confidence: 99%

CancerSEA: a cancer single-cell state atlas

Yuan

Yan

Zhang

et al. 2018

Nucleic Acids Research

572

454

View full text Add to dashboard Cite

High functional heterogeneity of cancer cells poses a major challenge for cancer research. Single-cell sequencing technology provides an unprecedented opportunity to decipher diverse functional states of cancer cells at single-cell resolution, and cancer scRNA-seq datasets have been largely accumulated. This emphasizes the urgent need to build a dedicated resource to decode the functional states of cancer single cells. Here, we developed CancerSEA (http://biocc.hrbmu.edu.cn/CancerSEA/ or http://202.97.205.69/CancerSEA/), the first dedicated database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. CancerSEA portrays a cancer single-cell functional state atlas, involving 14 functional states (including stemness, invasion, metastasis, proliferation, EMT, angiogenesis, apoptosis, cell cycle, differentiation, DNA damage, DNA repair, hypoxia, inflammation and quiescence) of 41 900 cancer single cells from 25 cancer types. It allows querying which functional states are associated with the gene (or gene list) of interest in different cancers. CancerSEA also provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. In summary, CancerSEA provides a user-friendly interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of tens of thousands of cancer single cells and the corresponding PCGs/lncRNAs expression profiles.

show abstract

Section: Methodsmentioning

confidence: 99%

CancerSEA: a cancer single-cell state atlas

Yuan

Yan

Zhang

et al. 2018

Nucleic Acids Research

572

454

View full text Add to dashboard Cite

show abstract

“…However, this set contains genes associated with pluripotency, such as Nanog , Klf2 , Klf4 , Klf5 , Zfp42/Rex1 , Sox2 , Esrrb , Nr0b1 , Dppa5a , and Zfp462 (Table S2), arguing for a delayed or restrained differentiation potential of Cited2 -depleted ESC. We also compared the set of genes upregulated in Cited2 -depleted cells with publicly available transcriptomics datasets related to stem cells using StemMapper 32 . This analysis confirmed that upregulated genes at D4 of differentiation in Cited2 -control cells distinguish between different cell lineages (Fig.…”

Section: Resultsmentioning

confidence: 99%

Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants

et al. 2019

Self Cite

View full text Add to dashboard Cite

Mutations and inadequate methylation profiles of CITED2 are associated with human congenital heart disease (CHD). In mouse, Cited2 is necessary for embryogenesis, particularly for heart development, and its depletion in embryonic stem cells (ESC) impairs cardiac differentiation. We have now determined that Cited2 depletion in ESC affects the expression of transcription factors and cardiopoietic genes involved in early mesoderm and cardiac specification. Interestingly, the supplementation of the secretome prepared from ESC overexpressing CITED2, during the onset of differentiation, rescued the cardiogenic defects of Cited2 -depleted ESC. In addition, we demonstrate that the proteins WNT5A and WNT11 held the potential for rescue. We also validated the zebrafish as a model to investigate cited2 function during development. Indeed, the microinjection of morpholinos targeting cited2 transcripts caused developmental defects recapitulating those of mice knockout models, including the increased propensity for cardiac defects and severe death rate. Importantly, the co-injection of anti- cited2 morpholinos with either CITED2 or WNT5A and WNT11 recombinant proteins corrected the developmental defects of Cited2-morphants. This study argues that defects caused by the dysfunction of Cited2 at early stages of development, including heart anomalies, may be remediable by supplementation of exogenous molecules, offering the opportunity to develop novel therapeutic strategies aiming to prevent CHD.

show abstract

“…Stem cell fate decisions, including the determination of cellular identity, are intimately linked to gene expression networks with each decision driven by wide-spread transcriptional changes ( Walker et al, 2007 ; Julian et al, 2013 , 2017b ; Julian and Blais, 2015 ; Pinto et al, 2018 ; Abdolhosseini et al, 2019 ; Wells and Choi, 2019 ). Transcriptional regulation does not function in isolation, however.…”

Section: Metabolic Organelle Network Regulate Stem Cell Fatementioning

confidence: 99%

Organelle Cooperation in Stem Cell Fate: Lysosomes as Emerging Regulators of Cell Identity

Julian

Stanford

2020

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

Regulation of stem cell fate is best understood at the level of gene and protein regulatory networks, though it is now clear that multiple cellular organelles also have critical impacts. A growing appreciation for the functional interconnectedness of organelles suggests that an orchestration of integrated biological networks functions to drive stem cell fate decisions and regulate metabolism. Metabolic signaling itself has emerged as an integral regulator of cell fate including the determination of identity, activation state, survival, and differentiation potential of many developmental, adult, disease, and cancer-associated stem cell populations and their progeny. As the primary adenosine triphosphate-generating organelles, mitochondria are well-known regulators of stem cell fate decisions, yet it is now becoming apparent that additional organelles such as the lysosome are important players in mediating these dynamic decisions. In this review, we will focus on the emerging role of organelles, in particular lysosomes, in the reprogramming of both metabolic networks and stem cell fate decisions, especially those that impact the determination of cell identity. We will discuss the inter-organelle interactions, cell signaling pathways, and transcriptional regulatory mechanisms with which lysosomes engage and how these activities impact metabolic signaling. We will further review recent data that position lysosomes as critical regulators of cell identity determination programs and discuss the known or putative biological mechanisms. Finally, we will briefly highlight the potential impact of elucidating mechanisms by which lysosomes regulate stem cell identity on our understanding of disease pathogenesis, as well as the development of refined regenerative medicine, biomarker, and therapeutic strategies.

show abstract

StemMapper: a curated gene expression database for stem cell lineage analysis

Cited by 28 publications

References 33 publications

CancerSEA: a cancer single-cell state atlas

CancerSEA: a cancer single-cell state atlas

Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants

Organelle Cooperation in Stem Cell Fate: Lysosomes as Emerging Regulators of Cell Identity

Contact Info

Product

Resources

About