Personalized differential expression analysis in triple-negative breast cancer.

Identification of individual-level differentially expressed genes (DEGs) is a pre-step for the analysis of disease-specific biological mechanisms and precision medicine. Previous algorithms cannot balance accuracy and sufficient statistical power. Herein, RankCompV2, designed for identifying population-level DEGs based on relative expression orderings, was adjusted to identify individual-level DEGs. Furthermore, an optimized version of individual-level RankCompV2, named as RankCompV2.1, was designed based on the assumption that the rank positions of genes and relative rank differences of gene pairs would influence the identification of individual-level DEGs. In comparison to other individualized analysis algorithms, RankCompV2.1 performed better on statistical power, computational efficiency, and acquired coequal accuracy in both simulation and real paired cancer-normal data from ten cancer types. Besides, single sample GSEA and Gene Set Variation Analysis analysis showed that pathways enriched with up-regulated and down-regulated genes presented higher and lower enrichment scores, respectively. Furthermore, we identified 16 genes that were universally deregulated in 966 triple-negative breast cancer (TNBC) samples and interacted with Food and Drug Administration (FDA)-approved drugs or antineoplastic agents, indicating notable therapeutic targets for TNBC. In addition, we also identified genes with highly variable deregulation status and used these genes to cluster TNBC samples into three subgroups with different prognoses. The subgroup with the poorest outcome was characterized by down-regulated immune-regulated pathways, signal transduction pathways, and apoptosis-related pathways. Protein-protein interaction network analysis revealed that OAS family genes may be promising drug targets to activate tumor immunity in this subgroup. In conclusion, RankCompV2.1 is capable of identifying individual-level DEGs with high accuracy and statistical power, analyzing mechanisms of carcinogenesis and exploring therapeutic strategy.

Integrated multi-omics and machine learning approach reveals lipid metabolic biomarkers and signaling in age-related meibomian gland dysfunction.

Meibomian gland dysfunction (MGD) is a prevalent inflammatory disorder of the ocular surface that significantly impacts patients' vision and quality of life. The underlying mechanism of aging and MGD remains largely uncharacterized. The aim of this work is to investigate lipid metabolic alterations in age-related MGD (ARMGD) through integrated proteomics, lipidomics and machine learning (ML) approach. For this purpose, we collected samples of female mouse meibomian glands (MGs) dissected from eyelids at age two months (n = 9) and two years (n = 9) for proteomic and lipidomic profilings using the liquid chromatography with tandem mass spectrometry (LC-MS/MS) method. To further identify ARMGD-related lipid biomarkers, ML model was established using the least absolute shrinkage and selection operator (LASSO) algorithm. For proteomic profiling, 375 differentially expressed proteins were detected. Functional analyses indicated the leading role of cholesterol biosynthesis in the aging process of MGs. Several proteins were proposed as potential biomarkers, including lanosterol synthase (Lss), 24-dehydrocholesterol reductase (Dhcr24), and farnesyl diphosphate farnesyl transferase 1 (Fdft1). Concomitantly, lipidomic analysis unveiled 47 lipid species that were differentially expressed and clustered into four classes. The most notable age-related alterations involved a decline in cholesteryl esters (ChE) levels and an increase in triradylglycerols (TG) levels, accompanied by significant differences in their lipid unsaturation patterns. Through ML construction, it was confirmed that ChE(26:0), ChE(26:1), and ChE(30:1) represent the most promising diagnostic molecules. The present study identified essential proteins, lipids, and signaling pathways in age-related MGD (ARMGD), providing a reference landscape to facilitate novel strategies for the disease transformation.

A thin film comprising silk peptide and cellulose nanofibrils implanting on the electrospun poly(lactic acid) fibrous scaffolds for biomedical reconstruction.

Conjunctival reconstruction using biocompatible polymers constitutes an effective treatment for conjunctival scarring and associated visual impairment. In this work, a thin film comprising silk peptide (SP), cellulose nanofibrils (CNF) and Ag nanoparticles (AgNPs) that implanted on the poly(lactic acid) (PLA) electrospun fibrous membranes (EFMs) was designed for biomedical reconstruction. SP and CNF as thin films can improve the surface hydrophilicity of the as-prepared scaffolds, which synergistically enhanced the biocompatibility. In in vivo experiments, the developed PLA EFMs modified with 3 wt% SP/CNF/AgNPs could be easily manipulated and transplanted onto conjunctival defects in rabbits, consequently accelerating the structural and functional restoration of the ocular surface in 12 days. Additionally, incorporation of 0.30 mg/g AgNPs efficiently reduced the topical application of antibiotics without causing infections. Thus, these resultant scaffolds could not only serve as useful alternatives for conjunctival engineering, but also prevent infections effectively with a very low content of AgNPs.

Nanotechnology-based ocular drug delivery systems: recent advances and future prospects.

Ocular drug delivery has constantly challenged ophthalmologists and drug delivery scientists due to various anatomical and physiological barriers. Static and dynamic ocular barriers prevent the entry of exogenous substances and impede therapeutic agents' active absorption. This review elaborates on the anatomy of the eye and the associated constraints. Followed by an illustration of some common ocular diseases, including glaucoma and their current clinical therapies, emphasizing the significance of drug therapy in treating ocular diseases. Subsequently, advances in ocular drug delivery modalities, especially nanotechnology-based ocular drug delivery systems, are recommended, and some typical research is highlighted. Based on the related research, systematic and comprehensive characterizations of the nanocarriers are summarized, hoping to assist with future research. Besides, we summarize the nanotechnology-based ophthalmic drugs currently on the market or still in clinical trials and the recent patents of nanocarriers. Finally, inspired by current trends and therapeutic concepts, we provide an insight into the challenges faced by novel ocular drug delivery systems and further put forward directions for future research. We hope this review can provide inspiration and motivation for better design and development of novel ophthalmic formulations.

Long-Acting Protective Ocular Surface by Instilling Adhesive Dual-Antiviral Nanoparticles.

The eye is susceptible to viral infections, causing severe ocular symptoms or even respiratory diseases. Methods capable of protecting the eye from external viral invasion in a long-term and highly effective way are urgently needed but have been proved to be extremely challenging. Here, a strategy of forming a long-acting protective ocular surface is described by instilling adhesive dual-antiviral nanoparticles. Taking pseudotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a model virus, antiviral agent-loaded nanoparticles are coated with a "double-lock" hybrid cell membrane abundant with integrin-ß1 and angiotensin converting enzyme II (ACE2). After instillation, the presence of integrin-ß1 endows coated nanoparticles with steady adhesion via specific binding to Arg-Gly-Asp sequence on the fibronectin of ocular epithelium, achieving durable retention on the ocular surface. In addition to loaded inhibitors, the exposure of ACE2 can trap SARS-CoV-2 and subsequently neutralize the associated spike protein, playing a dual antiviral effect of the resulting nanoparticles. Adhesive dual-antiviral nanoparticles enabled by coating with a "double-lock" hybrid cell membrane could be a versatile platform for topical long-acting protection against viral infection of the eye.

Direct oral mucosal epithelial transplantation supplies stem cells and promotes corneal wound healing to treat refractory persistent corneal epithelial defects.

Persistent corneal epithelial defects (PED) can lead to irreversible blindness, seriously affecting the social function and life quality of these patients. When it comes to refractory PED, such as limbal stem cell deficiency (LSCD), that does not respond to standard managements, stem cell therapy is an ideal method. Oral mucosal epithelium (OME) abundant with stem cells within the base, is a promising autologous biomaterial, with much resemblance to corneal epithelial structures. In this experiment, uncultured autologous rat OME was directly applied to alkali burned corneas. Clinical evaluations and histological analyses showed that the transplantation accelerated the healing process, presenting faster re-epithelization and better formation of corneal epithelial barrier. To further investigate the therapeutic mechanism, oral epithelium was transplanted to de-epithelialized cornea in vitro for organ culture. It could be observed that the oral epithelial cells could migrate to the corneal surface and form smooth and stratified epithelium. Immunofluorescence staining results showed that the re-formed epithelium derived from OME, maintained stemness and transformed to corneal epithelial phenotype to some extent. Corneal stroma may provide the suitable microenvironment to promote the trans-differentiation of oral stem cells. Thus, both in vivo and in vitro experiments suggested that oral epithelium could play a positive role in treating refractory PED.

Injectable bio-responsive hydrogel for therapy of inflammation related eyelid diseases.

Eyelid plays a vital role in protecting the eye from injury or infection. Inflammation related eyelid diseases, such as blepharitis, are the most common ocular disorders that affect human's vision and quality of life. Due to the physiological barriers and anatomical structures of the eye, the bioavailability of topical administrated therapeutics is typically less than 5%. Herein, we developed a bio-responsive hydrogel drug delivery system using a generally recognized as safe compound, triglycerol monostearate (TG-18), for in-situ eyelid injection with sustained therapeutics release. In vitro, drug release and disassembly time of Rosiglitazone loaded hydrogel (Rosi-hydrogel) were estimated in the presence or absence of MMP-9, respectively. Moreover, the disassembly of TG-18 hydrogel was evaluated with 9-month-old and 12-month-old mice in vivo. Owing to the bio-responsive nature of Rosi-hydrogel, the on-demand Rosiglitazone release is achieved in response to local enzymes. These findings are proved by further evaluation in the age-related meibomian gland dysfunction mice model, and the bio-responsive hydrogel is used as an in-situ injection to treat eyelid diseases. Taken together, the in-situ eyelid injection with sustained drug release opens a window for the therapy of inflammation related eyelid diseases.

Subconjunctival Injection of Regulatory T Cells Potentiates Corneal Healing Via Orchestrating Inflammation and Tissue Repair After Acute Alkali Burn.

Purpose: This study aimed to investigate the therapeutic effects and underlying mechanisms of locally delivered regulatory T cells (Tregs) on acute corneal wound healing after alkali burn. Methods: After corneal alkali burn, the mice were injected subconjunctivally with regulatory T cells (Tregs) isolated from syngeneic mice. The wound healing process was monitored by clinical manifestation, flow cytometry, and enzyme-linked immunosorbent assay (ELISA). As amphiregulin (Areg) was significantly upregulated, its reparative function in injured corneas was suggested. The hypothesis was further verified via loss- and gain-of-function experiments by administrating the antibody of Areg (anti-Areg) and recombinant Areg (rmAreg). Results: Subconjunctivally injected Tregs rapidly migrated to injured corneas. The mice treated with Tregs showed prominently reduced corneal opacity, alleviated edema, and faster re-epithelialization compared with the control group. Mechanistically, Treg treatment led to suppressed infiltration of inflammatory cells, along with improved proliferation and inhibited apoptosis of corneal epithelial cells. Tregs expressed upregulated functional markers, including Areg. Expectantly, the levels of Areg in corneas were dramatically higher in the Treg injection group, in line with better corneal restoration. Additional experiments showed that the administration of anti-Areg blunted the reparative effect of Tregs, while exogenous Areg enhanced it. Treg-treated corneas also exhibited less neovascularization and fibrosis at a later reconstruction stage of corneal repair. Conclusions: The findings showed that the subconjunctival injection of Tregs effectively promoted corneal wound healing by inhibiting excessive inflammation and enhancing epithelial regeneration, with an indispensable reparative role of Areg. Subsequent complications of corneal vascularization and fibrosis were therefore reduced.

Exploitation of human mesenchymal stromal cell derived matrix towards the structural and functional restoration of the ocular surface.

Conjunctival restoration is indispensable to help maintain the ocular surface microenvironment by secreting lubricative mucins. However, conventional amniotic membrane transplantation therapy has many limitations in its application due to risks involved with disease transmission and alloreactivity. As decellularized tissues have been frequently used for tissue engineering and adipose mesenchymal stem cells (ADMSCs) have been acknowledged for their low immunogenicity, we fabricated a decellularized matrix of adipose-derived mesenchymal stromal cells (DMA) to study the therapeutic potential of DMA in healing conjunctival defects. In the present study, the fabricated DMA, with certain thickness, exhibited transplantation operability in vivo. When applied in conjunctival defect rabbit models, the sheet of DMA played a substantial role in providing structural support without causing cosmetic difference. Moreover, DMA displayed great superiority in promoting faster wound closure with better stratified epithelium containing more goblet cells than the amniotic membranes (AMs). Mechanistically, compared with the tissue culture plates (TCPs) and TCPs coated with collagen or fibronectin (two of the main components of DMA), DMA exhibited its unique property in maintaining the stem cells of CjECs in an undifferentiated state, which is highly essential for long-term conjunctival reconstruction. In addition, DMA effectively enhanced the proliferation of CjECs by activating stronger phosphorylation of the Akt signaling pathway, the results of which were further verified in the in vivo experiment via the histological examination of p-Akt levels in reconstructed conjunctival epithelium by DMA. Thus, the decellularized matrix of ADMSCs depicts a promising conjunctival substitute in ocular reconstruction.

Evaluation of chronic ocular sequelae in patients with symblepharon caused by ocular burns.

AIM: To evaluate chronic ocular sequelae in patients with symblepharon caused by ocular burns and propose an objective grading system. METHODS: This was a retrospective, single-center clinical study. Patients with symblepharon caused by ocular burns at least six months later were assessed. Chronic ocular sequelae were classified into 3 categories (eyelid, conjunctiva, and cornea) and 9 chronic ocular sequelae [friction factors, exposure factors, conjunctival hyperemia, length of symblepharon, scope of adhesion, lacrimal area adhesion, loss of the palisades of Vogt (POV), corneal neovascularization, and corneal opacification]. Each ocular sequela was graded from 0 to 3, depending on the increasing severity. The 9 ocular sequelae were evaluated to obtain the total severity score for each eye. The total severity score was defined as Grade I (1-9), Grade II (10-18), and Grade III (19-27). Moreover, the correlation between the severity of chronic ocular sequelae and visual acuity, surgical strategy, and the prognosis was analyzed, respectively. RESULTS: Cases of 79 eyes with symblepharon caused by ocular burns were included in this study. Of these, 20 (25.32%) were defined as Grade I, 43 (54.43%) as Grade II, and 16 (20.25%) as Grade III. Eyes with a high total severity score had reduced visual acuity, required complicated surgery strategies, and poor prognosis (P<0.001). Multivariate regression analysis showed that the scope of adhesion, corneal opacification, and corneal neovascularization significantly affected visual acuity, surgical strategy, and prognosis (all P<0.001). CONCLUSION: The evaluation of chronic ocular sequelae enabled the development of an objective grading system for patients with symblepharon caused by ocular burns. This grading system can be applied to guide the treatment and predict the prognosis.

Corrigendum: 3D-Printed Poly-Caprolactone Scaffolds Modified With Biomimetic Extracellular Matrices for Tarsal Plate Tissue Engineering.

[This corrects the article DOI: 10.3389/fbioe.2020.00219.].

Trehalose attenuates TGF-ß1-induced fibrosis of hSCFs by activating autophagy.

Conjunctival fibrosis is a process of extracellular matrix accumulation and the appearance of myofibroblasts in subconjunctival fibroblasts induced by injury or inflammation, which can significantly reduce the filtration efficiency of glaucoma filtration surgery. In this study, autophagy was confirmed to be involved in regulating the fibrosis of human subconjunctival fibroblasts (hSCFs) induced by TGF-ß1. Following the addition of rapamycin, we detected that autophagy activation could reduce the increased expression level of αSMA and the accumulation of extracellular matrix component proteins namely fibronectin and type I collagen induced by TGF-ß1 via the inhibition of SMAD2 phosphorylation. Following the addition of HCQ, the inhibition of autophagy aggravated TGF-ß1-induced fibrosis of hSCFs. We further verified that trehalose, a safe clinical drug, could alleviate TGF-ß1-induced fibrosis of hSCFs by activating autophagy and that these effects could be blocked by autophagy inhibition. In summary, autophagy was shown to be involved in the regulation of TGF-ß1-induced fibrosis of hSCFs, which provided a novel perspective for exploring the progression of this lesion. More importantly, the protective effects of trehalose on TGF-ß1-induced fibrosis of hSCFs were mediated by the activation of autophagy and could provide possible new approaches for the clinical treatment of conjunctival fibrosis.

3D-Printed Poly-Caprolactone Scaffolds Modified With Biomimetic Extracellular Matrices for Tarsal Plate Tissue Engineering.

Tarsal plate regeneration has always been a challenge in the treatment of eyelid defects. The commonly used clinical treatments such as hard palate mucosa grafts cannot achieve satisfactory repair effects. Tissue engineering has been considered as a promising technology. However, tarsal plate tissue engineering is difficult to achieve due to its complex structure and lipid secretion function. Three-dimensional (3D) printing technology has played a revolutionary role in tissue engineering because it can fabricate complex scaffolds through computer aided design (CAD). In this study, it was novel in applying 3D printing technology to the fabrication of tarsal plate scaffolds using poly-caprolactone (PCL). The decellularized matrix of adipose-derived mesenchymal stromal cells (DMA) was coated on the surface of the scaffold, and its biofunction was further studied. Immortalized human SZ95 sebocytes were seeded on the scaffolds so that neutral lipids were secreted for replacing meibocytes. In vitro experiments revealed excellent biocompatibility of DMA-PCL scaffolds with sebocytes. In vivo experiments revealed excellent sebocytes proliferation on the DMA-PCL scaffolds. Meanwhile, sebocytes seeded on the scaffolds secreted abundant neutral lipid in vitro and in vivo. In conclusion, a 3D-printed PCL scaffold modified with DMA was found to be a promising substitute for tarsal plate tissue engineering.

Surface modified electrospun poly(lactic acid) fibrous scaffold with cellulose nanofibrils and Ag nanoparticles for ocular cell proliferation and antimicrobial application.

Corneal and conjunctival infections are common ocular diseases, sometimes, causing severe and refractory drug-resistant bacteria infections. Fungal keratitis is a leading cause for blindness and traditional medical treatment is unsatisfactory. Thus, there is an urge to develop a new therapy to deal with these cases. In this study, we developed surface modified poly(lactic acid) (PLA) electrospun nanofibrous membranes (EFMs) with silver nanoparticles (AgNPs) and cellulose nanofibrils (CNF) as scaffolds for cell proliferation and antimicrobial application. The AgNPs with a very low content (below 0.1%) were easily anchored on the surface of PLA EFMs by CNF, which endowed the scaffold with hydrophilicity and antibacterial ability. The in-vitro cell co-culture experiments showed that the scaffold had great biocompatibility to ocular epithelial cells, especially the scaffolds coated by CNF, which significantly proliferated cells. Furthermore, the antibacterial activity could reach >95% inhibiting Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) due to the implantation of AgNPs, and the antifungal activity was also outstanding with most of the Fusarium spp. inhibited. Hence, the developed PLA EFMs with CNF and AgNPs are promising ocular bandages to promote cell proliferation and kill infectious pathogens, exhibiting potential applications in ocular wound healing in the future.

Novel Three-Dimensional Morphometry to Reassess Orbit Deformities Associated With Orbital-Periorbital Plexiform Neurofibroma.

BACKGROUND: Orbit deformities are usually found in neurofibromatosis type 1 patients, especially those with orbital-periorbital plexiform neurofibroma (OPPN). Unfortunately, current morphometry is complicated and, in some cases, cannot be performed on the deformed orbit due to the destruction of landmarks. Herein, we present a novel 3-dimensional (3D) morphometry for these orbital measurements. METHODS: We retrospectively reviewed 29 patients with OPPN, and another 29 disseminated cutaneous neurofibroma patients served as controls. All patients had undergone craniofacial computed tomography and 3D reconstruction. New morphometry was used to measure the area of the orbital rim (OR) and superior orbital fissure (SOF). RESULTS: For the 29 patients with OPPN, the area of the OR at the affected side was 14.18 ±â€Š3.50 cm, while the OR at the nonaffected side was 12.32 ±â€Š1.38 cm. In addition, the area of the SOF at the affected side was 5.37 ±â€Š5.75 cm, while that at the nonaffected side was 1.27 ±â€Š1.03 cm. The OR and SOF at the affected side are more likely to become enlarged compared with those at the nonaffected side. Among the 29 patients with OPPN, the novel morphometry could be performed in 19 cases (65.5%) that cannot be measured by previous morphometry. CONCLUSION: The novel morphometry is convenient and reproducible, which optimizes its application in pathologic cases, especially those involving deformed orbits.

Long-Term Results for a One-Stage Surgery Technique for Patients With Craniofacial Plexiform Neurofibroma.

BACKGROUND: Neurofibromatosis (NF) is an autosomal dominant genetic disorder, and NF type 1 (NF1) is one of the most common forms. Plexiform neurofibroma (PNF) is one of the characteristic expressions of NF1. The proper treatment for patients with craniofacial PNF is surgery. The evaluation methods for the surgical outcome of these patients are still controversial. As a consequence, a one-stage surgical technique and an appropriate evaluation method for patients with craniofacial PNF were discussed in this article. METHODS: This research is a retrospective study. Nine patients with craniofacial PNF were included in this study. They had undergone a one-stage surgical technique of tumor debulking and nasolabial fold reconstruction. Three methods had been applied to evaluate the surgical outcome. RESULTS: Significant improvement was observed in 8 patients. Eight patients were assessed by the relatively objective evaluation method. Obvious symmetry improvement was calculated using Mimics software in 7 patients. CONCLUSION: The surgical technique could achieve good surgical outcomes in both functional and cosmetic terms. Additionally, the relatively objective evaluation technique based on Mimics software could be a more convincing method for evaluating the surgical outcomes of craniofacial patients with PNF.