Nano genome altas (NGA) of body wide organ responses

Gel microspheres enhance the stemness of ADSCs by regulating cell-ECM interaction

The gel microsphere culture system (GMCS) showed various advantages for mesenchymal stem cell (MSC) expansion and delivery, such as high specific surface area, small and regular shape, extensive adjustability, and biomimetic properties. Although various technologies and materials have been developed to promote the development of gel microspheres, the differences in the biological status of MSCs between the GMCS and the traditional Petri dish culture system (PDCS) are still unknown, hindering gel microspheres from becoming a culture system as widely used as petri dishes. In the previous study, an excellent "all-in-one" GMCS has been established for the expansion of human adipose-derived MSCs (hADSCs), which showed convenient cell culture operation. Here, we performed transcriptome and proteome sequencing on hADSCs cultured on the "all-in-one" GMCS and the PDCS. We found that hADSCs cultured in the GMCS kept in an undifferentiation status with a high stemness index, whose transcriptome profile is closer to the adipose progenitor cells (APCs) in vivo than those cultured in the PDCS. Further, the high stemness status of hADSCs in the GMCS was maintained through regulating cell-ECM interaction. For application, bilayer scaffolds were constructed by osteo- and chondro-differentiation of hADSCs cultured in the GMCS and the PDCS. The effect of osteochondral regeneration of the bilayer scaffolds in the GMCS group was better than that in the PDCS group. This study revealed the high stemness and excellent functionality of MSCs cultured in the GMCS, which promoted the application of gel microspheres in cell culture and tissue regeneration.

Size- and Dose-Dependent Body-Wide Organ Transcriptomic Responses to Calcium Phosphate Nanomaterials

Nanomaterials are widely used in clinical practice. There are potential risks of body-wide infiltration due to their small size; however, the body-wide reliable risk assessment of nanoparticle infiltration is not fully studied and established. In this study, we demonstrated the size- and dose-dependent body-wide organ transcriptomic responses to calcium phosphate nanomaterials in vivo. In a mice model, a calcium phosphate nanocluster (amorphous calcium phosphate, ACP, ∼1 nm in diameter) and its crystallization product (ACP-M, ∼10 nm in diameter) in a series of doses was administrated systematically; multiorgan transcriptomics were then performed with tissues of heart, liver, spleen, lung, kidney, and brain to investigate the systematic effect of dose and size of nanomaterials on the whole body. The results presented gene expression trajectories correlated with the dose of the nanomaterials and tissue-specific risk effects in all detected tissues. For the dose-dependent tissue-specific risk effects, lung tissue exhibited the most significant risk signatures related to apoptosis, cell proliferation, and cell stress. The spleen showed the second most significant risk signatures associated with immune response and DNA damage. For the size-dependent tissue-specific risk effects, ACP nanomaterials could increase most of the tissue-specific risk effects of nanomaterials in multiple organs than larger calcium phosphate nanoparticles. Finally, we used the size- and dose-dependent body-wide organ transcriptomic responses/risks to nanomaterials as the standards and built up a risk prediction model to evaluate the risk of the local nanomaterials delivery. Thus, our findings could provide a size- and dose- dependent risk assessment scale of nanoparticles in the transcriptomic level. It could be useful for risk assessment of nanomaterials in the future.

Nano-omics: Frontier fields of fusion of nanotechnology

Nanotechnology, an emerging force, has infiltrated diverse domains like biomedical, materials, and environmental sciences. Nano-omics, an emerging fusion, combines nanotechnology with omics, boasting amplified sensitivity and resolution. This review introduces nanotechnology basics, surveys its recent strides in nano-omics, deliberates present challenges, and envisions future growth.

Biomaterial based implants caused remote liver fatty deposition through activated blood-derived macrophages

Understanding the biocompatibility of biomaterials is a prerequisite for the prediction of its clinical application, and the present assessments mainly rely on in vitro cell culture and in situ histopathology. However, remote organs responses after biomaterials implantation is unclear. Here, by leveraging body-wide-transcriptomics data, we performed in-depth systems analysis of biomaterials - remote organs crosstalk after abdominal implantation of polypropylene and silk fibroin using a rodent model, demonstrating local implantation caused remote organs responses dominated by acute-phase responses, immune system responses and lipid metabolism disorders. Of note, liver function was specially disturbed, defined as hepatic lipid deposition. Combining flow cytometry analyses and liver monocyte recruitment inhibition experiments, we proved that blood derived monocyte-derived macrophages in the liver underlying the mechanism of abnormal lipid deposition induced by local biomaterials implantation. Moreover, from the perspective of temporality, the remote organs responses and liver lipid deposition of silk fibroin group faded away with biomaterial degradation and restored to normal at end, which highlighted its superiority of degradability. These findings were further indirectly evidenced by human blood biochemical ALT and AST examination from 141 clinical cases of hernia repair using silk fibroin mesh and polypropylene mesh. In conclusion, this study provided new insights on the crosstalk between local biomaterial implants and remote organs, which is of help for future selecting and evaluating biomaterial implants with the consideration of whole-body response.

Systemic and single cell level responses to 1 nm size biomaterials demonstrate distinct biological effects revealed by multi-omics atlas

Although ultra-small nanoclusters (USNCs, < 2 nm) have immense application capabilities in biomedicine, the investigation on body-wide organ responses towards USNCs is scant. Here, applying a novel strategy of single-cell mass cytometry combined with Nano Genome Atlas of multi-tissues, we systematically evaluate the interactions between the host and calcium phosphate (CaP) USNCs at the organism level. Combining single-cell mass cytometry, and magnetic luminex assay results, we identify dynamic immune responses to CaP USNCs at the single cell resolution. The innate immune is initially activated and followed by adaptive immune activation, as evidenced by dynamic immune cells proportions. Furthermore, using Nano Genome Atlas of multi-tissues, we uncover CaP USNCs induce stronger activation of the immune responses in the cartilage and subchondral bone among the five local tissues while promote metabolic activities in the liver and kidney. Moreover, based on the immunological response profiles, histological evaluation of major organs and local tissue, and a body-wide transcriptomics, we demonstrate that CaP USNCs are not more hazardous than the Food and Drug Administration-approved CaP nanoparticles after 14 days of injection. Our findings provide valuable information on the future clinical applications of USNCs and introduce an innovative strategy to decipher the whole body response to implants.

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We described a new strategy to facilitate the analysis of body-wide systemic responses of CaP USNCs in vivo.

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At single-cell resolution, we decoded a dynamic immune atlas of CaP USNCs in the blood.

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Based on the body-wide transcriptomics view, the biological effect of CaP USNCs is organ/tissue specific.

Dual role of injectable curcumin-loaded microgels for efficient repair of osteoarthritic cartilage injury

Curcumin has been widely used for the treatment of age-associated diseases, and showed chondroprotective potential for post-traumatic osteoarthritis (OA). However, due to the irregular-shaped and large-sized defects on joint cartilage in degenerated OA, the in vivo delivery and therapeutic effect of curcumin for effective repair remain challenging. In this study, we first present a PEG-GelMA [Poly(Ethylene Glycol) Dimethacrylate-Gelatin Methacrylate, PGMs] hydrogel microgel-based curcumin delivery system for both improved anti-inflammatory and pro-regenerative effects in treatment for cartilage defects. The curcumin-loaded PGMs were produced by a microfluidic system based on light-induced gelation of gelatin methacrylate (GelMA). This PGMs embedding curcumin at a relative low dosage were demonstrated to promote the proliferation and chondrogenic differentiation of mesenchymal stem cells in vitro. More importantly, the PGMs were shown to attenuate the inflammatory response of chondrocytes under IL-1β stimulation. Lastly, the in vivo application of the injectable PGMs significantly promoted the repair of large-sized cartilage injury. These results confirmed that curcumin-loaded PGMs can not only enhance the chondroprotective efficacy under inflammatory conditions but also induce efficient cartilage regeneration. This study provides an advanced strategy with anti-inflammatory and pro-regenerative dual-role therapeutic for treatment of extensive cartilage injuries.

Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage

Endometrium undergoes repeated repair and regeneration during the menstrual cycle. Previous attempts using gene expression data to define the menstrual cycle failed to come to an agreement. Here we used single-cell RNA sequencing data of C57BL/6J mice uteri to construct a novel integrated cell atlas of mice uteri from the regenerative endometrium to the maturational endometrium at the single-cell level, providing a more accurate cytological-based elucidation for the changes that occurred in the endometrium during the estrus cycle. Based on the expression levels of proliferating cell nuclear antigen, differentially expressed genes, and gene ontology terms, we delineated in detail the transitions of epithelial cells, stromal cells, and immune cells that happened during the estrus cycle. The transcription factors that shaped the differentiation of the mononuclear phagocyte system had been proposed, being Mafb, Irf7, and Nr4a1. The amounts and functions of immune cells varied sharply in two stages, especially NK cells and macrophages. We also found putative uterus tissue-resident macrophages and identified potential endometrial mesenchymal stem cells (high expression of Cd34, Pdgfrb, Aldh1a2) in vivo. The cell atlas of mice uteri presented here would improve our understanding of the transitions that occurred in the endometrium from the regenerative endometrium to the maturational endometrium. With the assistance of a normal cell atlas as a reference, we may identify morphologically unaffected abnormalities in future clinical practice. Cautions would be needed when adopting our conclusions, for the limited number of mice that participated in this study may affect the strength of our conclusions.

In vitro to in vivo extrapolation to support the development of the next generation risk assessment (NGRA) strategy for nanomaterials

There is growing interest in developing novel strategies to support assessment of human health risks due to chemicals. Regulatory and decision-making agencies have recommended that non-animal-based alternatives should be applied whenever possible instead of experimentation on living animals. These alternative methods are beneficial because they are ethical, inexpensive, and rapid. Herein, we review recent activities aimed at developing in vitro to in vivo extrapolation (IVIVE) models as a part of the Next Generation Risk Assessment (NGRA) of nanomaterials. In this context, we show the adverse outcome pathway (AOP)-based methodology for the identification of mechanistically relevant events serving as biomarkers for the targeted selection of in vitro assays. Considered events need to be biologically plausible, regulatory relevant, and crucial for the examination of occurrence of adverse outcomes. The promising advantages of using high-throughout-based omics data are highlighted. Furthermore, the application of 3D in vitro models and nano genome atlases to study nanoparticle toxicity is briefly summarized. Additionally, the challenges related to the extrapolation of in vitro doses into in vivo-relevant responses are presented. We also discuss the limitations of models applied thus far to study the fate of chemicals in the human body, which exist due to the lack of available knowledge regarding transformations of nanomaterials occurring in biological systems.

Engineered adipose-derived stem cells with IGF-1-modified mRNA ameliorates osteoarthritis development

BACKGROUND

Osteoarthritis (OA), a prevalent degenerative disease characterized by degradation of extracellular matrix (ECM), still lacks effective disease-modifying therapy. Mesenchymal stem cells (MSCs) transplantation has been regarded as the most promising approach for OA treatment while engrafting cells alone might not be adequate for effective regeneration. Genetic modification has been used to optimize MSC-based therapy; however, there are still significant limitations that prevent the clinical translation of this therapy including low efficacy and safety concerns. Recently, chemically modified mRNA (modRNA) represents a promising alternative for the gene-enhanced MSC therapy. In this regard, we hypothesized that adipose derived stem cells (ADSCs) engineered with modRNA encoding insulin-like growth factor 1 (IGF-1) were superior to native ADSCs on ameliorating OA development.

METHODS

Mouse ADSCs were acquired from adipose tissue and transfected with modRNAs. First, the kinetics and efficacy of modRNA-mediated gene transfer in mouse ADSCs were analyzed in vitro. Next, we applied an indirect co-culture system to analyze the pro-anabolic potential of IGF-1 modRNA engineered ADSCs (named as IGF-1-ADSCs) on chondrocytes. Finally, we evaluated the cell retention and chondroprotective effect of IGF-1-ADSCs in vivo using fluorescent labeling, histology and immunohistochemistry.

RESULTS

modRNA transfected mouse ADSCs with high efficiency (85 ± 5%) and the IGF-1 modRNA-transfected ADSCs facilitated burst-like production of bio-functional IGF-1 protein. In vitro, IGF-1-ADSCs induced increased anabolic markers expression of chondrocytes in inflammation environment compared to untreated ADSCs. In a murine OA model, histological and immunohistochemical analysis of knee joints harvested at 4 weeks and 8 weeks after OA induction suggested IGF-1-ADSCs had superior therapeutic effect over native ADSCs demonstrated by lower histological OARSI score and decreased loss of cartilage ECM.

CONCLUSIONS

These findings collectively supported the therapeutic potential of IGF-1-ADSCs for clinical OA management and cartilage repair.

“Musical dish” efficiently induces osteogenic differentiation of mesenchymal stem cells through music derived micro‐stretch with variable frequency

Nonuniform microstretching (NUMS) naturally occurs in real bone tissues in vivo, but its profound effects have not been identified yet. In order to explore the biological effects of NUMS and static stretch (uniform stretch [US]) on cells, a new “musical dish” device was developed. Musical signal was used to provide NUMS to cells. More stress fibers, arranging along the long axis of cells, were formed throughout the cells under NUMS, compared with US and untreated control group, although cell morphology did not show any alteration. Whole transcriptome sequencing revealed enhanced osteogenic differentiation of cells after NUMS treatment. Cells in the NUMS group showed a higher expression of bone‐related genes, while genes related to stemness and other lineages were down‐regulated. Our results give insights into the biological effects of NUMS and US on stem cell osteogenic differentiation, suggesting beneficial effects of micromechanical stimulus for osteogenesis. The newly developed device provides a basis for the development of NUMS derived rehabilitation technology to promote bone healing.

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials

Toxicogenomics (TGx) approaches are increasingly applied to gain insight into the possible toxicity mechanisms of engineered nanomaterials (ENMs). Omics data can be valuable to elucidate the mechanism of action of chemicals and to develop predictive models in toxicology. While vast amounts of transcriptomics data from ENM exposures have already been accumulated, a unified, easily accessible and reusable collection of transcriptomics data for ENMs is currently lacking. In an attempt to improve the FAIRness of already existing transcriptomics data for ENMs, we curated a collection of homogenized transcriptomics data from human, mouse and rat ENM exposures in vitro and in vivo including the physicochemical characteristics of the ENMs used in each study.

Classification of four distinct osteoarthritis subtypes with a knee joint tissue transcriptome atlas

The limited molecular classifications and disease signatures of osteoarthritis (OA) impede the development of prediagnosis and targeted therapeutics for OA patients. To classify and understand the subtypes of OA, we collected three types of tissue including cartilage, subchondral bone, and synovium from multiple clinical centers and constructed an extensive transcriptome atlas of OA patients. By applying unsupervised clustering analysis to the cartilage transcriptome, OA patients were classified into four subtypes with distinct molecular signatures: a glycosaminoglycan metabolic disorder subtype (C1), a collagen metabolic disorder subtype (C2), an activated sensory neuron subtype (C3), and an inflammation subtype (C4). Through ligand-receptor crosstalk analysis of the three knee tissue types, we linked molecular functions with the clinical symptoms of different OA subtypes. For example, the Gene Ontology functional term of vasculature development was enriched in the subchondral bone-cartilage crosstalk of C2 and the cartilage-subchondral bone crosstalk of C4, which might lead to severe osteophytes in C2 patients and apparent joint space narrowing in C4 patients. Based on the marker genes of the four OA subtypes identified in this study, we modeled OA subtypes with two independent published RNA-seq datasets through random forest classification. The findings of this work contradicted traditional OA diagnosis by medical imaging and revealed distinct molecular subtypes in knee OA patients, which may allow for precise diagnosis and treatment of OA.

Nanomaterial-based scaffolds for bone tissue engineering and regeneration

The global incidence of bone tissue injuries has been increasing rapidly in recent years, making it imperative to develop suitable bone grafts for facilitating bone tissue regeneration. It has been demonstrated that nanomaterials/nanocomposites scaffolds can more effectively promote new bone tissue formation compared with micromaterials. This may be attributed to their nanoscaled structural and topological features that better mimic the physiological characteristics of natural bone tissue. In this review, we examined the current applications of various nanomaterial/nanocomposite scaffolds and different topological structures for bone tissue engineering, as well as the underlying mechanisms of regeneration. The potential risks and toxicity of nanomaterials will also be critically discussed. Finally, some considerations for the clinical applications of nanomaterials/nanocomposites scaffolds for bone tissue engineering are mentioned.