Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but does not capture their spatial distribution nor reveal local networks of intercellular communication acting in ...situ. A suite of recently developed techniques that localize RNA within tissue, including multiplexed in situ hybridization and in situ sequencing (here defined as high-plex RNA imaging) and spatial barcoding, can help address this issue. However, no method currently provides as complete a scope of the transcriptome as does scRNA-seq, underscoring the need for approaches to integrate single-cell and spatial data. Here, we review efforts to integrate scRNA-seq with spatial transcriptomics, including emerging integrative computational methods, and propose ways to effectively combine current methodologies.
Objective
To investigate the expression of miR-217 and HIF-1α/VEGF pathway in patients with diabetic foot ulcer (DFU) and its effect on angiogenesis in DFU rats.
Methods
The serum levels of miR-217, ...HIF-1α and VEGF were detected in DFU and simple diabetes mellitus (DM) patients, and healthy controls. DFU rat models were established and treated with miR-217 inhibitors and/or HIF-1α siRNA. The ulcer healing of DFU rats was observed. Besides, ELISA method was performed to detect the serum level of HIF-1α, VEGF and inflammatory factors, immunohistochemical (IHC) method to test the micro-vessel density (MVD), as well as qRT-PCR and Western blot to determine expressions of miR-217, HIF-1α, VEGF, VEGFR2, eNOS, MMP-2, and MMP-9 in tissues.
Results
The serum levels of miR-217 were up-regulated while HIF-1α and VEGF were down-regulated in DFU patients and rats when compared with DM and healthy controls (all
P
< 0.05). Dual-luciferase reporter gene assay confirmed that
HIF
-
1α
was the direct target gene of miR-217. DFU rats treated with miR-217 inhibitors had decreased foot ulcer area and accelerated ulcer healing, with significantly reduced inflammatory factors (IL-1β, TNF-α and IL-6), as well as elevated HIF-1α and VEGF (all
P
< 0.05); meanwhile, they remarkably increased the MVD in foot dorsum wound tissues and the protein expressions of HIF-1α, VEGF, VEGFR2, eNOS, MMP-2, and MMP-9 (all
P
< 0.05).
Conclusion
Inhibiting miR-217 could up-regulate HIF-1α/VEGF pathway to promote angiogenesis and ameliorate inflammation of DFU rats, thereby effectively advancing the healing of ulcerated area.
The unique immunomodulatory properties of mesenchymal stem cells (MSCs) make them an invaluable cell type for the repair of tissue/ organ damage caused by chronic inflammation or autoimmune ...disorders. Although they hold great promise in the treatment of immune disorders such as graft versus host disease (GvHD) and allergic disorders, there remain many challenges to overcome before their widespread clinical application. An understanding of the biological properties of MSCs will clarify the mechanisms of MSC-based transplantation for immunomodulation. In this review, we summarize the preclinical and clinical studies of MSCs from different adult tissues, discuss the current hurdles to their use and propose the future development of pluripotent stem cell-derived MSCs as an approach to immunomodulation therapy.
Correlated multiple testing is widely performed in genetic research, particularly in multilocus analyses of complex diseases. Failure to control appropriately for the effect of multiple testing will ...either result in a flood of false-positive claims or in true hits being overlooked. Cheverud proposed the idea of adjusting correlated tests as if they were independent, according to an 'effective number' (M(eff)) of independent tests. However, our experience has indicated that Cheverud's estimate of the Meff is overly large and will lead to excessively conservative results. We propose a more accurate estimate of the M(eff), and design M(eff)-based procedures to control the experiment-wise significant level and the false discovery rate. In an evaluation, based on both real and simulated data, the M(eff)-based procedures were able to control the error rate accurately and consequently resulted in a power increase, especially in multilocus analyses. The results confirm that the M(eff) is a useful concept in the error-rate control of correlated tests. With its efficiency and accuracy, the M(eff) method provides an alternative to computationally intensive methods such as the permutation test.
To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging ...from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.
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•Profiling of 10 human skin SCCs and matched normals via scRNA-seq, ST, and MIBI•Tumor-specific keratinocytes (TSKs) reside within a fibrovascular niche at leading edges•Distinct ligand-receptor and spatial niche associations for tumor and stromal cells.•Subpopulation essential tumorigenic gene networks defined by in vivo CRISPR screening
Integration of high-dimensional multi-omics approaches to characterize human cutaneous squamous cell carcinoma identifies a tumor-specific keratinocyte population as well as the immune infiltrates and heterogeneity at tumor leading edges.
Heritage co-creation is a complex undertaking that involves the formation of cultural clusters and the collaborative creation of cultural value. However, implementing such co-creation is challenging ...due to various impact factors, and current technological approaches do not enable the formation of cultural clusters and co-creation simultaneously. To address this issue, this paper proposes a solution that incorporates the concept of meta-design with Web 3.0 enabling technologies to build a regenerative system that does not impose restrictions on the target audience and can be reseeded through user-generated content (UGC). The paper describes the method, process, and structure of a preliminary mock-up for co-creation, which includes a forum for communication and formation of cultural clusters, and a learning management system(LMS) that guides design-driven creation and facilitates the use of the co-design toolkits.
Aim
Skeletal muscle atrophy following prolonged immobilization (IM) is a catabolic state characterized by increased proteolysis and functional deterioration. Previous research indicates that discord ...of mitochondrial homoeostasis plays a critical role in muscle atrophy. We hypothesized that muscle IM would activate the ubiquitin‐proteolysis, autophagy–lysosome (mitophagy) pathway, mitochondrial dynamics remodelling and apoptosis partially controlled by the FoxO signalling pathway.
Methods
Female FVB/N mice were randomly divided into five groups (n = 8 each): control (CON), IM with banding of one of the hindlimbs for 1, 2 and 3 weeks (1w‐, 2w‐ and 3w‐IM) and 2w‐IM followed by 1 week of remobilization (RM).
Results
Mitochondrial density and DNA copies in tibialis anterior (TA) muscle were reduced by approx. 80% (P < 0.05 for 2w‐IM; P < 0.01 for 3w‐IM), along with activation of FoxO3a, atrogin‐1 and MuRF1 following 2w‐ and 3w‐IM (P < 0.01). Protein markers of autophagy/mitophagy, such as beclin 1 (approx. 2.7‐fold; P < 0.01), LC3, ubiquitin‐binding adaptor (approx. 1.47‐fold; P < 0.01), Rheb (approx. 1.9‐fold; P < 0.05) and parkin (approx. 70%; P < 0.05), were all increased by IM and remained activated after RM, whereas BNIP3 and PINK1 levels were decreased by IM (P < 0.05), but elevated upon RM (P < 0.01). IM decreased Mfn2 expression (approx. 50%; P < 0.01) and increased Fis‐1 expression (approx. 2.4‐fold; P < 0.05). Muscle apoptosis indicator Bax/Bcl2 ratio was elevated at 2w‐ to 3w‐IM (approx. 3.7‐fold; P < 0.01), whereas caspase‐3 activity was five‐ to sixfold higher (P < 0.01) and remained threefold higher above CON (P < 0.05).
Conclusion
Our data indicate that IM‐induced mitochondrial deterioration is associated with altered protein expressions in the autophagic/mitophagic pathway, more fragmented mitochondrial network and activation of apoptosis partly under the influence of FoxO3 activation.
Mitochondrial Ca2+ signaling, which is strongly dependent on the mitochondrial Ca2+ uniporter (MCU) complex, has a series of key roles in physiopathological processes, including energy metabolism, ...reactive oxygen species (ROS) production and cell apoptosis. However, a mechanistic understanding of how the mitochondrial Ca2+ signaling is remodeled and its functional roles remains greatly limited in cancers, especially in hepatocellular carcinoma. Here we demonstrated that the MCU complex was dysregulated in hepatocellular carcinoma (HCC) cells and significantly correlated with metastasis and poor prognosis of HCC patients. Upregulation of MCU clearly enhanced the Ca2+ uptake into mitochondria, which significantly promoted ROS production by downregulating nicotinamide adenine dinucleotide+ (NAD+)/reduced form of nicotinamide adenine dinucleotid (NADH) ratio and the NAD+-dependent deacetylase activity of sirtuin 3 to inhibit superoxide dismutase 2 (SOD2) activity. Moreover, our data indicated that the MCU-dependent mitochondrial Ca2+ uptake promotes matrix metalloproteinase-2 activity and cell motility by ROS-activated c-Jun N-terminal kinase pathway, and thus contributed to the increased ability of invasion and migration in vitro and intrahepatic and distal lung metastasis in vivo of HCC cells. In addition, treatment with the mitochondrial Ca2+-buffering protein parvalbumin significantly suppressed ROS production and the ability of HCC metastasis. Our study uncovers a mechanism that links the remodeling of mitochondrial Ca2+ homeostasis to ROS production, and provides evidence supporting a metastasis-promoting role for the MCU-dependent mitochondrial Ca2+ uptake in HCC. Our findings suggest that the mitochondrial Ca2+ uptake machinery may potentially be a novel therapeutic target for HCC metastasis.
Oxidative stress (OS) is one of the responsible factors for causing renal diseases. For the treatment or prevention of the renal disease, antioxidants use could be a hopeful therapeutic mediation as ...they block the oxidative reaction along with inflammatory process. Wogonin (Wog) is a plant flavonoid, a pharmacologically active component of
Georgi (Huang Qui), which exhibits antioxidant activity. In this investigation, we explored the nephroprotective activity of Wog on cadmium (Cd)-induced nephron toxicity in rats. Administering (10 and 20 mg/kg) intraperitoneally diminished Cd-induced anomalies in kidney histology and creatinine and serum urea levels. Wog therapy reduced the Cd-influenced generation of inflammatory mediators, inclusive of tumor necrosis factor alpha, interleukin 6, and interleukin 1 beta. Western blot analysis demonstrated that Wog abolished proinflammatory nuclear factor-kappa B (NF-κB) p65 stimulation, phosphorylation of p38 mitogen-activated protein kinases (MAPKs). In all, Wog demonstrated antioxidative and anti-inflammatory effects in Cd- intoxicated rats by obstructing OS and activation of NF-κB via restricting the stimulation of upstream kinases inclusive of MAPKs.
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