Single‐cell RNA sequencing redefines the mesenchymal cell landscape of mouse endometrium

Kirkwood, Phoebe M.; Gibson, Douglas A; Smith, J. F.; Wilson-Kanamori, John; Kelepouri, Olympia; Esnal-Zufiaurre, Arantza; Dobie, Ross; Henderson, Neil C.; Saunders, Philippa T. K.

doi:10.1096/fj.202002123r

Cited by 53 publications

(81 citation statements)

References 61 publications

(111 reference statements)

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“…7 ). ABCC9 has previously been shown to be a marker of vascular mural cells (e.g., pericytes and smooth muscle cells)[ 2 , 5 , 10 , 30 , 64 ] and the protein product has been implicated in modulating blood flow [ 45 , 51 , 61 ]. In terms of highly penetrant genetic variants, ABCC9 toxic gain-of-function mutations are linked to Cantu Syndrome, a complex phenotype that includes tortuous cerebral blood vessel patterns [ 31 , 32 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of genes (TMEM106B, GRN, ABCC9, KCNMB2, and APOE) implicated in risk for LATE-NC and hippocampal sclerosis provides pathogenetic insights: a retrospective genetic association study

Dugan

Nelson

Katsumata

et al. 2021

acta neuropathol commun

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Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is the most prevalent subtype of TDP-43 proteinopathy, affecting up to 1/3rd of aged persons. LATE-NC often co-occurs with hippocampal sclerosis (HS) pathology. It is currently unknown why some individuals with LATE-NC develop HS while others do not, but genetics may play a role. Previous studies found associations between LATE-NC phenotypes and specific genes: TMEM106B, GRN, ABCC9, KCNMB2, and APOE. Data from research participants with genomic and autopsy measures from the National Alzheimer’s Coordinating Center (NACC; n = 631 subjects included) and the Religious Orders Study and Memory and the Rush Aging Project (ROSMAP; n = 780 included) were analyzed in the current study. Our goals were to reevaluate disease-associated genetic variants using newly collected data and to query whether the specific genotype/phenotype associations could provide new insights into disease-driving pathways. Research subjects included in prior LATE/HS genome-wide association studies (GWAS) were excluded. Single nucleotide variants (SNVs) within 10 kb of TMEM106B, GRN, ABCC9, KCNMB2, and APOE were tested for association with HS and LATE-NC, and separately for Alzheimer’s pathologies, i.e. amyloid plaques and neurofibrillary tangles. Significantly associated SNVs were identified. When results were meta-analyzed, TMEM106B, GRN, and APOE had significant gene-based associations with both LATE and HS, whereas ABCC9 had significant associations with HS only. In a sensitivity analysis limited to LATE-NC + cases, ABCC9 variants were again associated with HS. By contrast, the associations of TMEM106B, GRN, and APOE with HS were attenuated when adjusting for TDP-43 proteinopathy, indicating that these genes may be associated primarily with TDP-43 proteinopathy. None of these genes except APOE appeared to be associated with Alzheimer’s-type pathology. In summary, using data not included in prior studies of LATE or HS genomics, we replicated several previously reported gene-based associations and found novel evidence that specific risk alleles can differentially affect LATE-NC and HS.

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Section: Discussionmentioning

confidence: 99%

Analysis of genes (TMEM106B, GRN, ABCC9, KCNMB2, and APOE) implicated in risk for LATE-NC and hippocampal sclerosis provides pathogenetic insights: a retrospective genetic association study

Dugan

Nelson

Katsumata

et al. 2021

acta neuropathol commun

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“…Analysis of EPCAM+ cells resulted in identification of 9 subpopulations of epithelial cells based on cluster analysis and comparisons to genes previously identified as being expressed in different locations including the lumen (Yang et al, 2021) and glands (Foxa2, (Kelleher et al, 2017). When we combined our eGFP+ and EPCAM+ scRNAseq datasets three broad groups of cell types was present: epithelial, perivascular, fibroblast and epithelial with the repair-specific transient population of cells appearing to be a distinct fibroblast subpopulation which on trajectory analysis appeared to form a 'bridge' between the previously identified fibroblast clusters (Kirkwood et al, 2021) and the new epithelial datasets. Based on previous reports of the importance of endometrial progenitor populations in endometrial repair and identification of cells with stem-like properties in a perivascular location (Gargett et al, 2016) we had initially anticipated this cell type might be the one that was mobilised to undergo MET however the new data suggested this assumption was incorrect.…”

Section: Discussionmentioning

confidence: 80%

“…Population restricted cell sorting was used to isolate CD31-/CD45-/GFP+(PDGFRβ+) cells prior to single cell sequencing. In cycling mice we have previously reported GFP+ cells are restricted to the stromal compartment of the endometrium (Kirkwood et al, 2021). scRNAseq was used to generate a dataset for each timepoint and these were then integrated for downstream cluster and differential gene expression analysis.…”

Section: Single Cell Rna Sequencing Identifies Novel Mesenchymal Cell Subpopulations Unique To 'Repairing' Tissue In a Mouse Model Of Endmentioning

confidence: 99%

“…This strategy resulted in identification of 8 transcriptionally distinct clusters of GFP+ cells (Figure 1B). The expression of canonical phenotypic gene markers for mesenchymal, perivascular and fibroblast cell populations previously identified in control/cycling mouse endometrium was used to assign putative identities to each cluster (Kirkwood et al, 2021). This strategy identified 3 perivascular populations (V, P1, P2; expression of Mcam, Cspg4, Rgs4, Acta2) and 5 fibroblast subpopulations (F1-5; expression of Pdgfra, Cd34, Fbln1/2, Mfap4/5, Col1a1).…”

Section: Single Cell Rna Sequencing Identifies Novel Mesenchymal Cell Subpopulations Unique To 'Repairing' Tissue In a Mouse Model Of Endmentioning

confidence: 99%

“…In Pdgfrb-BAC-eGFP reporter mice, eGFP expression is driven by the regulatory sequences of the Pdgfrb gene and is therefore expressed by all cells in which the promoter is active. Details of these transgenic mice and their use for studies on the endometrium of cycling mice have been previously described (Kirkwood et al, 2021). These mice were originally obtained from GENSAT and deposited in MMRRC-STOCK Tg(Pdgfrb-EGFP)JN169Gsat/Mmucd, 031796-UCD).…”

Section: Mouse Linesmentioning

confidence: 99%

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Single cell RNA sequencing and lineage tracing confirm mesenchyme to epithelial transformation (MET) contributes to repair of the endometrium at menstruation

Kirkwood

Gibson

Shaw

et al. 2021

Preprint

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The human endometrium experiences repetitive cycles of tissue wounding characterised by piecemeal shedding of the surface epithelium and rapid restoration of tissue homeostasis. In this study we used a validated mouse model of endometrial repair in combination with three transgenic lines of mice to investigate whether epithelial cells that become incorporated into the newly formed luminal epithelium have their origins in one or more of the mesenchymal cell types present in the stromal compartment of the cycling endometrium. Using scRNAseq we identified a novel population of PDGFRb+ cells that arose in the endometrium in response to endometrial breakdown/repair. These cells expressed genes usually considered specific to epithelial cells and in silico trajectory analysis suggested they arose from stromal fibroblasts and were in transition to becoming epithelial cells. To confirm our hypothesis we used a lineage tracing strategy to compare the fate of stromal fibroblasts (PDGFRa+) and stromal perivascular cells (NG2+). We demonstrate for the first time that stromal fibroblasts can undergo a mesenchyme to epithelial transformation and become incorporated into the re-epithelialised luminal surface of the repaired tissue. This study is the first to discover a novel population of wound-responsive, plastic endometrial stromal fibroblasts that contribute to restoration of tissue integrity during endometrial repair. These findings form a platform for comparisons both to endometrial pathologies which involve a fibrotic response (Ashermans syndrome, endometriosis) as well as other mucosal tissues which have a variable response to wounding.

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Microfluidic systems in clinical diagnosis

Lapizco‐Encinas

Zhang

2022

Electrophoresis

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The use of microfluidic devices is highly attractive in the field of biomedical and clinical assessments, as their portability and fast response time have become crucial in providing opportune therapeutic treatments to patients. The applications of microfluidics in clinical diagnosis and point‐of‐care devices are continuously growing. The present review article discusses three main fields where miniaturized devices are successfully employed in clinical applications. The quantification of ions, sugars, and small metabolites is examined considering the analysis of bodily fluids samples and the quantification of this type of analytes employing real‐time wearable devices. The discussion covers the level of maturity that the devices have reached as well as cost‐effectiveness. The analysis of proteins with clinical relevance is presented and organized by the function of the proteins. The last section covers devices that can perform single‐cell metabolomic and proteomic assessments. Each section discusses several strategically selected recent reports on microfluidic devices successfully employed for clinical assessments, to provide the reader with a wide overview of the plethora of novel systems and microdevices developed in the last 5 years. In each section, the novel aspects and main contributions of each reviewed report are highlighted. Finally, the conclusions and future outlook section present a summary and speculate on the future direction of the field of miniaturized devices for clinical applications.

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Single‐cell RNA sequencing redefines the mesenchymal cell landscape of mouse endometrium

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 53 publications

References 61 publications

Analysis of genes (TMEM106B, GRN, ABCC9, KCNMB2, and APOE) implicated in risk for LATE-NC and hippocampal sclerosis provides pathogenetic insights: a retrospective genetic association study

Analysis of genes (TMEM106B, GRN, ABCC9, KCNMB2, and APOE) implicated in risk for LATE-NC and hippocampal sclerosis provides pathogenetic insights: a retrospective genetic association study

Single cell RNA sequencing and lineage tracing confirm mesenchyme to epithelial transformation (MET) contributes to repair of the endometrium at menstruation

Microfluidic systems in clinical diagnosis

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