Improving the Photodynamic Activity of Water-Soluble Porphyrin-Polysaccharide Complexes by Folic Acid Modification.

Studies have shown that folate receptors are highly expressed in various cancer cells. Here, we synthesized folic acid-conjugated pullulan (FAPL) as a solubilizing agent to improve the photodynamic activity of porphyrin derivative-polysaccharide complexes. The porphyrin derivative-FAPL complex exhibited long-term stability in an aqueous solution, attributed to the folic acid modification. Furthermore, in vitro and in vivo experiments highlighted the enhanced photodynamic activity of the porphyrin derivative-FAPL complex toward 4T1 breast-cancer cells, compared with the activities of the porphyrin derivative-pullulan complex and Photofrin. This enhanced activity is attributed to the improvement of intracellular uptake by the folate receptor.

Microarray transcriptome datasets of maternal-zygotic DNA methyltransferase 3aa -/- zebrafish during early developmental stages.

DNA methylation is an epigenetic regulator mediated by DNA methyltransferases (Dnmts). The methylation is involved in control of gene expression in vertebrates. It has been reported that there are mainly two types of de novo Dnmts, Dnmt3a and Dnmt3b, in mammals. These two Dnmts function in DNA methylation in the distinct or overlapping genomic regions. The zebrafish homologs of mammalian Dnmt3a are Dnmt3aa and Dnmt3ab. We generated a maternal-zygotic dnmt3aa deficient mutant (MZdnmt3aa) to identify the specific target regions for DNA methylation in the zebrafish genome and their function in the developmental process. Microarray analysis revealed alterations in gene expression by knock-out of dnmt3aa in early zebrafish development. Microarray datasets were produced from samples at five different developmental stages: 1-2 cell, shield, 5-somite, 1-day post fertilization (dpf), and 2 dpf. Herein, we present novel raw and processed transcriptome datasets generated by analysis of the MZdnmt3aa -/- mutant. The raw microarray data are available through the Gene Expression Omnibus (GEO), accession number GSE202646. These transcriptome data may be useful for comparing differences in gene expression among species of Dnmt3a mutants and for analyzing human diseases caused by DNMT3A such as acute myelogenous leukemia (AML).

CHRNA1 and its correlated-myogenesis/cell cycle genes are prognosis-related markers of metastatic melanoma.

Nicotinic acetylcholine receptors (CHRNs) expression and their critical role in various types of cancer have been reported. However, it is still unclear which CHRNs and their associated genes play essential roles in metastasis in melanoma patients. Here, we performed bioinformatics analyses on publicly available bulk RNA sequencing (RNA-seq) data of patients with melanoma to identify the CHRNs highly expressed in metastatic melanoma. We found that CHRNA1 was highly expressed in metastatic melanoma samples compared to primary melanoma samples and was strongly associated with CHRNB1 and CHRNG. These muscle-type CHRNs (CHRNA1, CHRNB1, and CHRNG) were correlated with the ZEB1 and Rho/ROCK pathway-related genes in metastatic melanoma samples. Pairwise correlations and enrichment analyses revealed that CHRNA1 was significantly associated with myogenesis/muscle contraction and cell cycle genes. Kaplan-Meier curves illustrated the involvement of CHRNA1, four of its correlated genes (DES, FLNC, CDK1, and CDC20), and the myogenesis gene signature in the prognosis of melanoma patients. Following the bulk RNA-seq analysis, single-cell RNA-seq (scRNA-seq) analysis showed that the CHRNA1-expressing melanoma cells are primarily metastatic and had high expression levels of CHRNB1, CHRNG, and myogenesis/cell cycle-related genes. Our bioinformatics analyses of the bulk RNA-seq and scRNA-seq data of patients with melanoma revealed that CHRNA1 and its correlated myogenesis/cell-related cycle genes are critical prognosis-related markers of metastatic melanoma.

Biomimetic antimicrobial polymers-Design, characterization, antimicrobial, and novel applications.

Biomimetic antimicrobial polymers have been an area of great interest as the need for novel antimicrobial compounds grows due to the development of resistance. These polymers were designed and developed to mimic naturally occurring antimicrobial peptides in both physicochemical composition and mechanism of action. These antimicrobial peptide mimetic polymers have been extensively investigated using chemical, biophysical, microbiological, and computational approaches to gain a deeper understanding of the molecular interactions that drive function. These studies have helped inform SARs, mechanism of action, and general physicochemical factors that influence the activity and properties of antimicrobial polymers. However, there are still lingering questions in this field regarding 3D structural patterning, bioavailability, and applicability to alternative targets. In this review, we present a perspective on the development and characterization of several antimicrobial polymers and discuss novel applications of these molecules emerging in the field. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.

Radiomic Analysis for Pretreatment Prediction of Recurrence Post-Radiotherapy in Cervical Squamous Cell Carcinoma Cancer.

BACKGROUND: The current study aims to predict the recurrence of cervical cancer patients treated with radiotherapy from radiomics features on pretreatment T1- and T2-weighted MR images. METHODS: A total of 89 patients were split into model training (63 patients) and model testing (26 patients). The predictors of recurrence were selected using the least absolute shrinkage and selection operator (LASSO) regression. The machine learning used neural network classifiers. RESULTS: Using LASSO analysis of radiomics, we found 25 features from the T1-weighted and 4 features from T2-weighted MR images, respectively. The accuracy was highest with the combination of T1- and T2-weighted MR images. The model performances with T1- or T2-weighted MR images were 86.4% or 89.4% accuracy, 74.9% or 38.1% sensitivity, 81.8% or 72.2% specificity, and 0.89 or 0.69 of the area under the curve (AUC). The model performance with the combination of T1- and T2-weighted MR images was 93.1% accuracy, 81.6% sensitivity, 88.7% specificity, and 0.94 of AUC. CONCLUSIONS: The radiomics analysis with T1- and T2-weighted MR images could highly predict the recurrence of cervix cancer after radiotherapy. The variation of the distribution and the difference in the pixel number at the peripheral and the center were important predictors.

Understanding Breast Cancers through Spatial and High-Resolution Visualization Using Imaging Technologies.

Breast cancer is the most common cancer affecting women worldwide. Although many analyses and treatments have traditionally targeted the breast cancer cells themselves, recent studies have focused on investigating entire cancer tissues, including breast cancer cells. To understand the structure of breast cancer tissues, including breast cancer cells, it is necessary to investigate the three-dimensional location of the cells and/or proteins comprising the tissues and to clarify the relationship between the three-dimensional structure and malignant transformation or metastasis of breast cancers. In this review, we aim to summarize the methods for analyzing the three-dimensional structure of breast cancer tissue, paying particular attention to the recent technological advances in the combination of the tissue-clearing method and optical three-dimensional imaging. We also aimed to identify the latest methods for exploring the relationship between the three-dimensional cell arrangement in breast cancer tissues and the gene expression of each cell. Finally, we aimed to describe the three-dimensional imaging features of breast cancer tissues using noninvasive photoacoustic imaging methods.

Methylome data derived from maternal-zygotic DNA methyltransferase 3aa-/- zebrafish.

Genomic DNA methylation is an epigenetic marker mediated by DNA methyltransferases (Dnmts); in vertebrates, it comprises of a maintenance DNA methyltransferase, Dnmt1, and two de novo DNA methyltransferases (Dnmt3a and Dnmt3b). In zebrafish, there are two homologs of the mammalian Dnmt3a: Dnmt3aa and Dnmt3ab. A knockout (KO) mutant of zebrafish dnmt3aa was generated using the CRISPR/Cas9 genome-editing system as a new model for DNA methylation research. Since zebrafish dnmt3aa KO mutants were viable and fertile, a maternal-zygotic dnmt3aa deficient mutant (MZdnmt3aa) was generated. We performed whole-genome bisulfite sequencing (WGBS) to reveal the DNA methylation profile using this mutant and identified genomic regions with altered CpG methylation as differentially methylated regions (DMRs) in this mutant compared to those in the wild-type fish. We provided novel raw and processed datasets using the MZdnmt3aa KO mutant, and the raw data of WGBS are available through the Gene Expression Omnibus (GEO), accession number GSE178690.

Analysis of Melanoma Gene Expression Signatures at the Single-Cell Level Uncovers 45-Gene Signature Related to Prognosis.

Since the current melanoma clinicopathological staging system remains restricted to predicting survival outcomes, establishing precise prognostic targets is needed. Here, we used gene expression signature (GES) classification and Cox regression analyses to biologically characterize melanoma cells at the single-cell level and construct a prognosis-related gene signature for melanoma. By analyzing publicly available scRNA-seq data, we identified six distinct GESs (named: "Anti-apoptosis", "Immune cell interactions", "Melanogenesis", "Ribosomal biogenesis", "Extracellular structure organization", and "Epithelial-Mesenchymal Transition (EMT)"). We verified these GESs in the bulk RNA-seq data of patients with skin cutaneous melanoma (SKCM) from The Cancer Genome Atlas (TCGA). Four GESs ("Immune cell interactions", "Melanogenesis", "Ribosomal biogenesis", and "Extracellular structure organization") were significantly correlated with prognosis (p = 1.08 × 10-5, p = 0.042, p = 0.001, and p = 0.031, respectively). We identified a prognostic signature of melanoma composed of 45 genes (MPS_45). MPS_45 was validated in TCGA-SKCM (HR = 1.82, p = 9.08 × 10-6) and three other melanoma datasets (GSE65904: HR = 1.73, p = 0.006; GSE19234: HR = 3.83, p = 0.002; and GSE53118: HR = 1.85, p = 0.037). MPS_45 was independently associated with survival (p = 0.002) and was proved to have a high potential for predicting prognosis in melanoma patients.

Identification of aberrant transcription termination at specific gene loci with DNA hypomethylated transcription termination sites caused by DNA methyltransferase deficiency.

CpG methylation of genomic DNA is a well-known repressive epigenetic marker in eukaryotic transcription, and DNA methylation of promoter regions is correlated with gene silencing. In contrast to the promoter regions, the function of DNA methylation during transcription termination remains to be elucidated. A recent study revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions in de novo methylation in the promoter and gene body regions, including transcription termination sites (TTSs), during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we performed bioinformatics analysis using six pre-existing Dnmt-/- mouse cell datasets: four types of neurons (three Dnmt3a-/- and one Dnmt1-/- mutants) and two types of embryonic fibroblasts (MEFs) (Dnmt3a-/- and Dnmt3b-/- mutants). Combined analyses using methylome and transcriptome data revealed that read counts downstream of hypomethylated TTSs were increased in three types of neurons (two Dnmt3a-/- and one Dnmt1-/- mutants). Among these, an increase in chimeric transcripts downstream of the TTSs was observed in Dnmt3a-/- mature olfactory sensory neurons and Dnmt3a-/- agouti-related peptide (protein)-producing neurons, thereby indicating that read-through occurs in hypomethylated TTSs at specific gene loci in these two mutants. Conversely, in Dnmt3a-/- MEFs, we detected reductions in read counts downstream of hypomethylated TTSs. These results indicate that the hypomethylation of TTSs can both positively and negatively regulate transcription termination, dependent on Dnmt and cell types. This study is the first to identify the aberrant termination of transcription at specific gene loci with DNA hypomethylated TTSs attributable to Dnmt deficiency.

3D in vitro co-culture disc for spatiotemporal image analysis of cancer-stromal cell interaction.

Assessing phenotypic changes in both cancer cells and surrounding cells, which construct the tumour microenvironment, is essential for understanding the role of bi-directional communication among cells in the tumorigenic process. Here, a 3D in vitro cancer-stroma co-culture system, a co-culture disc, was reported for the spatiotemporal image analysis of cancer-stromal cell interactions. Due to their centre-open disc structure, the lung cancer A549 spheroids could be co-cultured with a high concentration of fibroblasts, without gel shrinkage in the long term (>1 month). In the co-culture disc, some populations of applied normal human lung fibroblasts showed morphological and phenotypic changes into activated myofibroblasts (AMFs) with high expression of myo-fibrotic α-smooth muscle actin fibre in the cell, which is a well-known feature of cancer-associated fibroblasts. The AMFs appeared heterogeneously at the boundary of cancer spheroids, which could not be detected by standard mass analysis using a quantitative RT-qPCR system, and they led to A549 cancer cell migration. In addition, the effects of oncogenic or medicinal additives were quantitatively assessed by combining co-culture discs with image analysis. This system provides a new potential technique to analyse the complicated crosstalk among cancer tissue-constructing cells during the tumorigenic process and provides insight into applications for the quantitative evaluation of substances inducing tumorigenesis as well as drugs to prevent and inhibit cancer progression.

Synthetic Biomimetic Polymethacrylates: Promising Platform for the Design of Anti-Cyanobacterial and Anti-Algal Agents.

Extensive, uncontrolled growth of algae and cyanobacteria is an environmental, public health, economic, and technical issue in managing natural and engineered water systems. Synthetic biomimetic polymers have been almost exclusively considered antimicrobial alternatives to conventional antibiotics to treat human bacterial infections. Very little is known about their applicability in an aquatic environment. Here, we introduce synthetic biomimetic polymethacrylates (SBPs) as a cost-effective and chemically facile, flexible platform for designing a new type of agent suitable for controlling and mitigating photosynthetic microorganisms. Since SBPs are cationic and membranolytic in heterotrophic bacteria, we hypothesized they could also interact with negatively charged cyanobacterial or algal cell walls and membranes. We demonstrated that SBPs inhibited the growth of aquatic photosynthetic organisms of concern, i.e., cyanobacteria (Microcystis aeruginosa and Synechococcus elongatus) and green algae (Chlamydomonas reinhardtii and Desmodesmus quadricauda), with 50% effective growth-inhibiting concentrations ranging between 95 nM and 6.5 µM. Additionally, SBPs exhibited algicidal effects on C. reinhardtii and cyanocidal effects on picocyanobacterium S. elongatus and microcystin-producing cyanobacterium M. aeruginosa. SBP copolymers, particularly those with moderate hydrophobic content, induced more potent cyanostatic and cyanocidal effects than homopolymers. Thus, biomimetic polymers are a promising platform for the design of anti-cyanobacterial and anti-algal agents for water treatment.

Amphiphilic polymer therapeutics: an alternative platform in the fight against antibiotic resistant bacteria.

As we are on the cusp of the "post-antibiotic" era due to rapid spread of drug resistant bacteria, there is an urgent need for new antimicrobials that are not susceptible to bacterial resistance mechanisms. In this review, we will discuss the recent development of "polymer therapeutics" with antimicrobial activity. Learning from host-defence peptides, we propose the biomimetic design of synthetic polymers to target bacterial cell membranes, which act by compromising the membrane integrity. The discussion is extended to the future challenges and opportunities of antimicrobial polymers for clinical applications.

Author Correction: Anticancer polymers designed for killing dormant prostate cancer cells.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Anticancer polymers designed for killing dormant prostate cancer cells.

The discovery of anticancer therapeutics effective in eliminating dormant cells is a significant challenge in cancer biology. Here, we describe new synthetic polymer-based anticancer agents that mimic the mode of action of anticancer peptides. These anticancer polymers developed here are designed to capture the cationic, amphiphilic traits of anticancer peptides. The anticancer polymers are designed to target anionic lipids exposed on the cancer cell surfaces and act by disrupting the cancer cell membranes. Because the polymer mechanism is not dependent on cell proliferation, we hypothesized that the polymers were active against dormant cancer cells. The polymers exhibited cytotoxicity to proliferating prostate cancer. Importantly, the polymer killed dormant prostate cancer cells that were resistant to docetaxel. This study demonstrates a new approach to discover novel anticancer therapeutics.

Branched Poly(ethylene imine)s as Anti-algal and Anti-cyanobacterial Agents with Selective Flocculation Behavior to Cyanobacteria over Algae.

Poly(ethylene imine)s (PEIs) have been widely studied for biomedical applications, including antimicrobial agents against potential human pathogens. The interactions of branched PEIs (B-PEIs) with environmentally relevant microorganisms whose uncontrolled growth in natural or engineered environments causes health, economic, and technical issues in many sectors of water management are studied. B-PEIs are shown to be potent antimicrobials effective in controlling the growth of environmentally relevant algae and cyanobacteria with dual-functionality and selectivity. Not only did they effectively inhibit growth of both algae and cyanobacteria, mostly without causing cell death (static activity), but they also selectively flocculated cyanobacteria over algae. Thus, unmodified B-PEIs provide a cost-effective and chemically facile framework for the further development of effective and selective antimicrobial agents useful for control of growth and separation of algae and cyanobacteria in natural or engineered environments.

A Vascular Endothelial Growth Factor-Dependent Sprouting Angiogenesis Assay Based on an In Vitro Human Blood Vessel Model for the Study of Anti-Angiogenic Drugs.

Angiogenesis is the formation of new capillaries from pre-existing blood vessels and participates in proper vasculature development. In pathological conditions such as cancer, abnormal angiogenesis takes place. Angiogenesis is primarily carried out by endothelial cells, the innermost layer of blood vessels. The vascular endothelial growth factor-A (VEGF-A) and its receptor-2 (VEGFR-2) trigger most of the mechanisms activating and regulating angiogenesis, and have been the targets for the development of drugs. However, most experimental assays assessing angiogenesis rely on animal models. We report an in vitro model using a microvessel-on-a-chip. It mimics an effective endothelial sprouting angiogenesis event triggered from an initial microvessel using a single angiogenic factor, VEGF-A. The angiogenic sprouting in this model is depends on the Notch signaling, as observed in vivo. This model enables the study of anti-angiogenic drugs which target a specific factor/receptor pathway, as demonstrated by the use of the clinically approved sorafenib and sunitinib for targeting the VEGF-A/VEGFR-2 pathway. Furthermore, this model allows testing simultaneously angiogenesis and permeability. It demonstrates that sorafenib impairs the endothelial barrier function, while sunitinib does not. Such in vitro human model provides a significant complimentary approach to animal models for the development of effective therapies.

A 3D in vitro pericyte-supported microvessel model: visualisation and quantitative characterisation of multistep angiogenesis.

Angiogenesis, which refers to the formation of new blood vessels from already existing vessels, is a promising therapeutic target and a complex multistep process involving many different factors. Pericytes (PCs) are attracting attention as they are considered to make significant contributions to the maturation and stabilisation of newly formed vessels, although not much is known about the precise mechanisms involved. Since there is no single specific marker for pericytes, in vivo models may complicate PC identification and the study of PCs in angiogenesis would benefit from in vitro models recapitulating the interactions between PCs and endothelial cells (ECs) in a three-dimensional (3D) configuration. In this study, a 3D in vitro co-culture microvessel model incorporating ECs and PCs was constructed by bottom-up tissue engineering. Angiogenesis was induced in the manner of sprout formation by the addition of a vascular endothelial cell growth factor. It was found that the incorporation of PCs prevented expansion of the parent vessel diameter and enhanced sprout formation and elongation. Physical interactions between ECs and PCs were visualised by immunostaining and it disclosed that PCs covered the EC monolayer from its basal side in the parent vessel as well as angiogenic sprouts. Furthermore, the microvessels were visualized in 3D by using a non-invasive optical coherence tomography (OCT) imaging system and sprout features were quantitatively assessed. It revealed that the sprouts in EC-PC co-culture vessels were longer and tighter than those in EC mono-culture vessels. The combination of the microvessel model and the OCT system analysis can be useful for the visualisation and demonstration of the multistep process of angiogenesis, which incorporates PCs.

Bundle Gel Fibers with a Tunable Microenvironment for in Vitro Neuron Cell Guiding.

As scaffolds for neuron cell guiding in vitro, gel fibers with a bundle structure, comprising multiple microfibrils, were fabricated using a microfluidic device system by casting a phase-separating polymer blend solution comprising hydroxypropyl cellulose (HPC) and sodium alginate (Na-Alg). The topology and stiffness of the obtained bundle gel fibers depended on their microstructure derived by the polymer blend ratio of HPC and Na-Alg. High concentrations of Na-Alg led to the formation of small microfibrils in a one-bundle gel fiber and stiff characteristics. These bundle gel fibers permitted for the elongation of the neuron cells along their axon orientation with the long axis of fibers. In addition, human-induced pluripotent-stem-cell-derived dopaminergic neuron progenitor cells were differentiated into neuronal cells on the bundle gels. The bundle gel fibers demonstrated an enormous potential as cell culture scaffold materials with an optimal microenvironment for guiding neuron cells.

A Vascular Permeability Assay Using an In Vitro Human Microvessel Model Mimicking the Inflammatory Condition.

The vascular barrier is an important function of the endothelium and its dysfunction is involved in several diseases. The barrier function of the endothelial cell monolayer is governed by cell-cell, cell-extracellular matrix (cell-ECM) contacts, and inflammatory factors such as thrombin, histamine or vascular endothelial growth factor. Several in vivo and in vitro assays that measure the vascular permeability induced by these factors have been developed. However, they suffer limitations such as being challenging for assessing details of biological processes at a cellular level or lacking the architecture of a vessel, that raise the need for new methods. In vitro 3D model-based assays have thus been developed but assays for investigating compounds that protects the barrier function are lacking. Here we describe the development of an in vitro three-dimensional (3D) vascular endothelium model in which we can manipulate the endothelial barrier function and permeability to molecules, which have a molecular weight similar to human serum albumin, allowing to assess the protective effect of compounds. A microvessel was prepared by culturing human umbilical vein endothelial cells (HUVECs) within a collagen gel on a polydimethylsiloxane (PDMS) chip. Using fluorescein isothiocyanate (FITC)-conjugated dextran (70 kDa, FITC-dextran) and confocal fluorescence microscopy, we showed that the microvessel presented an effective barrier function. We were then able to induce the loss of this barrier function by treatment with the inflammatory factor thrombin. The loss of barrier function was quantified by the extravasation of FITC-dextran into collagen matrix. Furthermore, we were able to analyze the protective effect on the endothelial barrier function of the cyclic adenosine monophosphate (cAMP) analog, 8-pCPT-2'-O-Me-cAMP (also called 007). In an attempt to understand the effects of thrombin and 007 in our model, we analyzed the adherens junctions and cytoskeleton through immunostaining of the vascular endothelial cadherin and actin, respectively. Our assay method could be used to screen for compounds modulating the barrier function of endothelial cells, as well as investigating mechanistic aspects of barrier dysfunction.

Synthetic Random Copolymers as a Molecular Platform To Mimic Host-Defense Antimicrobial Peptides.

Synthetic polymers have been used as a molecular platform to develop host-defense antimicrobial peptide (AMP) mimetics which are effective in killing drug-resistant bacteria. In this topical review, we will discuss the AMP-mimetic design and chemical optimization strategies as well as the biological and biophysical implications of AMP mimicry by synthetic polymers. Traditionally, synthetic polymers have been used as a chemical means to replicate the chemical functionalities and physicochemical properties of AMPs (e.g., cationic charge, hydrophobicity) to recapitulate their mode of action. However, we propose a new perception that AMP-mimetic polymers are an inherently bioactive platform as whole molecules, which mimic more than the side chain functionalities of AMPs. The tunable nature and chemical simplicity of synthetic random polymers facilitate the development of potent, cost-effective, broad-spectrum antimicrobials. The polymer-based approach offers the potential for many antimicrobial applications to be used directly in solution or attached to surfaces to fight against drug-resistant bacteria.