scholarly journals Single Cell Transcriptomic Landscape of Diabetic Foot Ulcers

2021 ◽  
Author(s):  
Georgios Theocharidis ◽  
Beena E. Thomas ◽  
Debasree Sarkar ◽  
William JR Pilcher ◽  
Bhakti Dwivedi ◽  
...  
Keyword(s):  
Wound Healing ◽  
Single Cell ◽  
Single Cells ◽  
Macrophage Polarization ◽  
Cell Types ◽  
Deep Wound ◽  
Preferential Localization ◽  
M1 Macrophage ◽  
Diabetic Wound Healing ◽  
Healing Wounds

AbstractTo understand the diabetic wound healing microenvironment, we profiled 174,962 single cells from foot, forearm, and PBMCs using single-cell RNA sequencing (scRNASeq) approach. Our analysis shows enrichment of a unique population of fibroblasts overexpressing MMP1, MMP3, MMP11, HIF1A, CHI3L1, and TNFAIP6 genes and M1 macrophage polarization in the DFU patients with healing wounds. Further, scRNASeq of spatially separated samples from same patient and spatial transcriptomics (ST) revealed preferential localization of these healing associated fibroblasts toward deep wound/ulcer bed as compared to wound edge or non-wounded skin. ST also validated our findings of higher enrichment of M1 macrophages in healers and M2 macrophages in non-healers. Our analysis provides deep insights into the wound healing microenvironment, identifying cell types that could be critical in promoting DFU healing, and may inform novel therapeutic approaches for DFU treatment.

scholarly journals Single cell transcriptomic landscape of diabetic foot ulcers

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Georgios Theocharidis ◽  
Beena E. Thomas ◽  
Debasree Sarkar ◽  
Hope L. Mumme ◽  
William J. R. Pilcher ◽  
...  
Keyword(s):  
Single Cell ◽  
Diabetic Foot ◽  
Mononuclear Cells ◽  
Single Cells ◽  
Macrophage Polarization ◽  
Cell Types ◽  
Peripheral Blood Mononuclear ◽  
Preferential Localization ◽  
M1 Macrophage ◽  
Healing Wounds

AbstractDiabetic foot ulceration (DFU) is a devastating complication of diabetes whose pathogenesis remains incompletely understood. Here, we profile 174,962 single cells from the foot, forearm, and peripheral blood mononuclear cells using single-cell RNA sequencing. Our analysis shows enrichment of a unique population of fibroblasts overexpressing MMP1, MMP3, MMP11, HIF1A, CHI3L1, and TNFAIP6 and increased M1 macrophage polarization in the DFU patients with healing wounds. Further, analysis of spatially separated samples from the same patient and spatial transcriptomics reveal preferential localization of these healing associated fibroblasts toward the wound bed as compared to the wound edge or unwounded skin. Spatial transcriptomics also validates our findings of higher abundance of M1 macrophages in healers and M2 macrophages in non-healers. Our analysis provides deep insights into the wound healing microenvironment, identifying cell types that could be critical in promoting DFU healing, and may inform novel therapeutic approaches for DFU treatment.

scholarly journals Wound Healing: A Cellular Perspective

2019 ◽  
Vol 99 (1) ◽  
pp. 665-706 ◽  
Author(s):  
Melanie Rodrigues ◽  
Nina Kosaric ◽  
Clark A. Bonham ◽  
Geoffrey C. Gurtner
Keyword(s):  
Wound Healing ◽  
Single Cell ◽  
Wound Closure ◽  
Chronic Wounds ◽  
Cell Types ◽  
Skin Injury ◽  
Complex Processes ◽  
Cell Technologies ◽  
Cellular Recruitment ◽  
Healing Wounds

Wound healing is one of the most complex processes in the human body. It involves the spatial and temporal synchronization of a variety of cell types with distinct roles in the phases of hemostasis, inflammation, growth, re-epithelialization, and remodeling. With the evolution of single cell technologies, it has been possible to uncover phenotypic and functional heterogeneity within several of these cell types. There have also been discoveries of rare, stem cell subsets within the skin, which are unipotent in the uninjured state, but become multipotent following skin injury. Unraveling the roles of each of these cell types and their interactions with each other is important in understanding the mechanisms of normal wound closure. Changes in the microenvironment including alterations in mechanical forces, oxygen levels, chemokines, extracellular matrix and growth factor synthesis directly impact cellular recruitment and activation, leading to impaired states of wound healing. Single cell technologies can be used to decipher these cellular alterations in diseased states such as in chronic wounds and hypertrophic scarring so that effective therapeutic solutions for healing wounds can be developed.

scholarly journals Single-Cell RNA Sequencing Reveals Cellular and Transcriptional Changes Associated With M1 Macrophage Polarization in Hidradenitis Suppurativa

2021 ◽  
Vol 8 ◽  
Author(s):  
Paula Mariottoni ◽  
Simon W. Jiang ◽  
Courtney A. Prestwood ◽  
Vaibhav Jain ◽  
Jutamas Suwanpradid ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Hidradenitis Suppurativa ◽  
Macrophage Polarization ◽  
M1 Macrophage ◽  
Single Cell Rna Sequencing ◽  
Signaling Axis ◽  
Transcriptional Changes ◽  
Healing Wounds ◽  
Overlap Analysis

Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by recurrent abscesses, nodules, and sinus tracts in areas of high hair follicle and sweat gland density. These sinus tracts can present with purulent drainage and scar formation. Dysregulation of multiple immune pathways drives the complexity of HS pathogenesis and may account for the heterogeneity of treatment response in HS patients. Using transcriptomic approaches, including single-cell sequencing and protein analysis, we here characterize the innate inflammatory landscape of HS lesions. We identified a shared upregulation of genes involved in interferon (IFN) and antimicrobial defense signaling through transcriptomic overlap analysis of differentially expressed genes (DEGs) in datasets from HS skin, diabetic foot ulcers (DFUs), and the inflammatory stage of normal healing wounds. Overlap analysis between HS- and DFU-specific DEGs revealed an enrichment of gene signatures associated with monocyte/macrophage functions. Single-cell RNA sequencing further revealed monocytes/macrophages with polarization toward a pro-inflammatory M1-like phenotype and increased effector function, including antiviral immunity, phagocytosis, respiratory burst, and antibody-dependent cellular cytotoxicity. Specifically, we identified the STAT1/IFN-signaling axis and the associated IFN-stimulated genes as central players in monocyte/macrophage dysregulation. Our data indicate that monocytes/macrophages are a potential pivotal player in HS pathogenesis and their pathways may serve as therapeutic targets and biomarkers in HS treatment.

scholarly journals Inflammatory M1-like macrophages polarized by NK-4 undergo enhanced phenotypic switching to an anti-inflammatory M2-like phenotype upon co-culture with apoptotic cells

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Keizo Kohno ◽  
Satomi Koya-Miyata ◽  
Akira Harashima ◽  
Takahiko Tsukuda ◽  
Masataka Katakami ◽  
...  
Keyword(s):  
Wound Healing ◽  
Chronic Wounds ◽  
Macrophage Polarization ◽  
Phenotypic Switching ◽  
Apoptotic Cells ◽  
Phenotypic Switch ◽  
Inflammatory Phase ◽  
M1 Macrophage ◽  
Tnf Α ◽  
Anti Inflammatory

Abstract Background NK-4 has been used to promote wound healing since the early-1950s; however, the mechanism of action of NK-4 is unknown. In this study, we examined whether NK-4 exerts a regulatory effect on macrophages, which play multiple roles during wound healing from the initial inflammatory phase until the tissue regeneration phase. Results NK-4 treatment of THP-1 macrophages induced morphological features characteristic of classically-activated M1 macrophages, an inflammatory cytokine profile, and increased expression of the M1 macrophage-associated molecules CD38 and CD86. Interestingly, NK-4 augmented TNF-α production by THP-1 macrophages in combination with LPS, Pam3CSK4, or poly(I:C). Furthermore, NK-4 treatment enhanced THP-1 macrophage phagocytosis of latex beads. These results indicate that NK-4 drives macrophage polarization toward an inflammatory M1-like phenotype with increased phagocytic activity. Efferocytosis is a crucial event for resolution of the inflammatory phase in wound healing. NK-4-treated THP-1 macrophages co-cultured with apoptotic Jurkat E6.1 (Apo-J) cells switched from an M1-like phenotype to an M2-like phenotype, as seen in the inverted ratio of TNF-α to IL-10 produced in response to LPS. We identified two separate mechanisms that are involved in this phenotypic switch. First, recognition of phosphatidylserine molecules on Apo-J cells by THP-1 macrophages downregulates TNF-α production. Second, phagocytosis of Apo-J cells by THP-1 macrophages and activation of PI3K/Akt signaling pathway upregulates IL-10 production. Conclusion It is postulated that the phenotypic switch from a proinflammatory M1-like phenotype to an anti-inflammatory M2-like phenotype is dysregulated due to impaired efferocytosis of apoptotic neutrophils at the wound site. Our results demonstrate that NK-4 improves phagocytosis of apoptotic cells, suggesting its potential as a therapeutic strategy to resolve sustained inflammation in chronic wounds.

scholarly journals HiCImpute: A Bayesian Hierarchical Model for Identifying Structural Zeros and Enhancing Single Cell Hi-C Data.

2021 ◽  
Author(s):  
Qing Xie ◽  
Chengong Han ◽  
Victor Jin ◽  
Shili Lin
Keyword(s):  
Quality Improvement ◽  
Data Quality ◽  
Single Cell ◽  
Single Cells ◽  
High Sensitivity ◽  
Real Data ◽  
Cell Types ◽  
Sequencing Depth ◽  
2D Data ◽  
Structural Zeros

Single cell Hi-C techniques enable one to study cell to cell variability in chromatin interactions. However, single cell Hi-C (scHi-C) data suffer severely from sparsity, that is, the existence of excess zeros due to insufficient sequencing depth. Complicate things further is the fact that not all zeros are created equal, as some are due to loci truly not interacting because of the underlying biological mechanism (structural zeros), whereas others are indeed due to insufficient sequencing depth (sampling zeros), especially for loci that interact infrequently. Differentiating between structural zeros and sampling zeros is important since correct inference would improve downstream analyses such as clustering and discovery of subtypes. Nevertheless, distinguishing between these two types of zeros has received little attention in the single cell Hi-C literature, where the issue of sparsity has been addressed mainly as a data quality improvement problem. To fill this gap, in this paper, we propose HiCImpute, a Bayesian hierarchy model that goes beyond data quality improvement by also identifying observed zeros that are in fact structural zeros. HiCImpute takes spatial dependencies of scHi-C 2D data structure into account while also borrowing information from similar single cells and bulk data, when such are available. Through an extensive set of analyses of synthetic and real data, we demonstrate the ability of HiCImpute for identifying structural zeros with high sensitivity, and for accurate imputation of dropout values in sampling zeros. Downstream analyses using data improved from HiCImpute yielded much more accurate clustering of cell types compared to using observed data or data improved by several comparison methods. Most significantly, HiCImpute-improved data has led to the identification of subtypes within each of the excitatory neuronal cells of L4 and L5 in the prefrontal cortex.

scholarly journals Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

2020 ◽  
Author(s):  
Feng Tian ◽  
Fan Zhou ◽  
Xiang Li ◽  
Wenping Ma ◽  
Honggui Wu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Human Cell ◽  
Expression Profiles ◽  
Single Cells ◽  
Cell Types ◽  
List Type ◽  
Cell Type ◽  
Genomic Architecture ◽  
Gene Modules

SummaryBy circumventing cellular heterogeneity, single cell omics have now been widely utilized for cell typing in human tissues, culminating with the undertaking of human cell atlas aimed at characterizing all human cell types. However, more important are the probing of gene regulatory networks, underlying chromatin architecture and critical transcription factors for each cell type. Here we report the Genomic Architecture of Cells in Tissues (GeACT), a comprehensive genomic data base that collectively address the above needs with the goal of understanding the functional genome in action. GeACT was made possible by our novel single-cell RNA-seq (MALBAC-DT) and ATAC-seq (METATAC) methods of high detectability and precision. We exemplified GeACT by first studying representative organs in human mid-gestation fetus. In particular, correlated gene modules (CGMs) are observed and found to be cell-type-dependent. We linked gene expression profiles to the underlying chromatin states, and found the key transcription factors for representative CGMs.HighlightsGenomic Architecture of Cells in Tissues (GeACT) data for human mid-gestation fetusDetermining correlated gene modules (CGMs) in different cell types by MALBAC-DTMeasuring chromatin open regions in single cells with high detectability by METATACIntegrating transcriptomics and chromatin accessibility to reveal key TFs for a CGM

scholarly journals Novel formulation approaches for wound healing

2020 ◽  
Vol 11 (SPL4) ◽  
pp. 937-948
Author(s):  
Tanaji D Nandgude ◽  
Syed Nateque Naser
Keyword(s):  
Wound Healing ◽  
Healing Process ◽  
Cell Types ◽  
Wound Management ◽  
Wound Healing Process ◽  
Anatomic Structure ◽  
Tissue Integrity ◽  
Molecular Events ◽  
Acute Injuries ◽  
Healing Wounds

A wound is damage to the typical anatomic structure. Wound healing is an immediate therapeutic response to injury. It is a creation of the combined response of some cell types towards injury. Wound healing takes place by a sequence of molecular events which cooperate to fix tissue integrity and cell work. In typical healthy individual under ordinary conditions, these physiological events take place smoothly. Though sometimes, these molecular events are arrested, this brings about in struggle to heal. There is an assortment of approaches for the way toward managing and controlling both acute injuries (acute wounds) and ceaseless non-mending wounds (chronic non-healing wounds). The principal objective of these two cases is to achieve better-wound healing. Ideal formulations of wound healing should not only enhance the healing process but also reduce pain, infection and loss of electrolytes, proteins and liquids from the injury. A broad scope of items typically introduced with target various parts of the wound healing process depends on numerous types of wounds and novel polymers utilised for the conveyance of medications to both acute and ceaseless injuries. These include alginate, hydrocolloids, hydrofibers, polyurethane, and hydrogels. This article gives particular importance to different novel approaches in the management of wound healing. This review draws out the data and hopes to provide understanding into traditional, current and imminent techniques and methods for wound management.

scholarly journals Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Elliott Swanson ◽  
Cara Lord ◽  
Julian Reading ◽  
Alexander T Heubeck ◽  
Palak C Genge ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Single Cell ◽  
Human Peripheral Blood ◽  
Single Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Test Case ◽  
Cell Assays ◽  
Paired Measurement

Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, cellular responses to signals, and human disease. Recent advances have allowed paired capture of protein abundance and transcriptomic state, but a lack of epigenetic information in these assays has left a missing link to gene regulation. Using the heterogeneous mixture of cells in human peripheral blood as a test case, we developed a novel scATAC-seq workflow that increases signal-to-noise and allows paired measurement of cell surface markers and chromatin accessibility: integrated cellular indexing of chromatin landscape and epitopes, called ICICLE-seq. We extended this approach using a droplet-based multiomics platform to develop a trimodal assay that simultaneously measures transcriptomics (scRNA-seq), epitopes, and chromatin accessibility (scATAC-seq) from thousands of single cells, which we term TEA-seq. Together, these multimodal single-cell assays provide a novel toolkit to identify type-specific gene regulation and expression grounded in phenotypically defined cell types.

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