Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson’s disease

Parkinson’s disease (PD) is the second-most prevalent neurodegenerative disorder, characterized by the loss of dopaminergic neurons (mDA) in the midbrain. The underlying mechanisms are only partly understood and there is no treatment to reverse PD progression. Here, we investigated the disease mechanism using mDA neurons differentiated from human induced pluripotent stem cells (hiPSCs) carrying the ILE368ASN mutation within the PINK1 gene, which is strongly associated with PD. Single-cell RNA sequencing (RNAseq) and gene expression analysis of a PINK1-ILE368ASN and a control cell line identified genes differentially expressed during mDA neuron differentiation. Network analysis revealed that these genes form a core network, members of which interact with all known 19 protein-coding Parkinson’s disease-associated genes. This core network encompasses key PD-associated pathways, including ubiquitination, mitochondrial function, protein processing, RNA metabolism, and vesicular transport. Proteomics analysis showed a consistent alteration in proteins of dopamine metabolism, indicating a defect of dopaminergic metabolism in PINK1-ILE368ASN neurons. Our findings suggest the existence of a network onto which pathways associated with PD pathology converge, and offers an inclusive interpretation of the phenotypic heterogeneity of PD.

Pulmonary Mesenchymal Stem Cells in Mild Cases of COVID-19 Are Dedicated to Proliferation; In Severe Cases, They Control Inflammation, Make Cell Dispersion, and Tissue Regeneration

Mesenchymal stem cells (MSCs) are multipotent adult stem cells present in virtually all tissues; they have potent self-renewal capacity and differentiate into multiple cell types. For many reasons, these cells are a promising therapeutic alternative to treat patients with severe COVID-19 and pulmonary post-COVID sequelae. These cells are not only essential for tissue regeneration; they can also alter the pulmonary environment through the paracrine secretion of several mediators. They can control or promote inflammation, induce other stem cells differentiation, restrain the virus load, and much more. In this work, we performed single-cell RNA-seq data analysis of MSCs in bronchoalveolar lavage samples from control individuals and COVID-19 patients with mild and severe clinical conditions. When we compared samples from mild cases with control individuals, most genes transcriptionally upregulated in COVID-19 were involved in cell proliferation. However, a new set of genes with distinct biological functions was upregulated when we compared severely affected with mild COVID-19 patients. In this analysis, the cells upregulated genes related to cell dispersion/migration and induced the γ-activated sequence (GAS) genes, probably triggered by IFNGR1 and IFNGR2. Then, IRF-1 was upregulated, one of the GAS target genes, leading to the interferon-stimulated response (ISR) and the overexpression of many signature target genes. The MSCs also upregulated genes involved in the mesenchymal-epithelial transition, virus control, cell chemotaxis, and used the cytoplasmic RNA danger sensors RIG-1, MDA5, and PKR. In a non-comparative analysis, we observed that MSCs from severe cases do not express many NF-κB upstream receptors, such as Toll-like (TLRs) TLR-3, -7, and -8; tumor necrosis factor (TNFR1 or TNFR2), RANK, CD40, and IL-1R1. Indeed, many NF-κB inhibitors were upregulated, including PPP2CB, OPTN, NFKBIA, and FHL2, suggesting that MSCs do not play a role in the “cytokine storm” observed. Therefore, lung MSCs in COVID-19 sense immune danger and act protectively in concert with the pulmonary environment, confirming their therapeutic potential in cell-based therapy for COVID-19. The transcription of MSCs senescence markers is discussed.

The landscape of human tissue and cell type specific expression and co-regulation of senescence genes

Background Cellular senescence is a complex stress response that impacts cellular function and organismal health. Multiple developmental and environmental factors, such as intrinsic cellular cues, radiation, oxidative stress, oncogenes, and protein accumulation, activate genes and pathways that can lead to senescence. Enormous efforts have been made to identify and characterize senescence genes (SnGs) in stress and disease systems. However, the prevalence of senescent cells in healthy human tissues and the global SnG expression signature in different cell types are poorly understood. Methods This study performed an integrative gene network analysis of bulk and single-cell RNA-seq data in non-diseased human tissues to investigate SnG co-expression signatures and their cell-type specificity. Results Through a comprehensive transcriptomic network analysis of 50 human tissues in the Genotype-Tissue Expression Project (GTEx) cohort, we identified SnG-enriched gene modules, characterized SnG co-expression patterns, and constructed aggregated SnG networks across primary tissues of the human body. Our network approaches identified 51 SnGs highly conserved across the human tissues, including CDKN1A (p21)-centered regulators that control cell cycle progression and the senescence-associated secretory phenotype (SASP). The SnG-enriched modules showed remarkable cell-type specificity, especially in fibroblasts, endothelial cells, and immune cells. Further analyses of single-cell RNA-seq and spatial transcriptomic data independently validated the cell-type specific SnG signatures predicted by the network analysis. Conclusions This study systematically revealed the co-regulated organizations and cell type specificity of SnGs in major human tissues, which can serve as a blueprint for future studies to map senescent cells and their cellular interactions in human tissues.

Characterization of Luminescent Down-Shifting Spectral Conversion Effects on Silicon Solar Cells with Various Combinations of Eu-Doped Phosphors

Luminescent down-shifting (LDS) spectral conversion is a feasible approach to enhancing the short-wavelength response of single junction solar cells. This paper presents the optical and electrical characteristics of LDS spectral conversion layers containing a single species or two species of Eu-doped phosphors applied to the front surface of silicon solar cells via spin-on coating. The chemical composition, surface morphology, and fluorescence emission of the LDS layers were respectively characterized using energy-dispersive X-ray analysis, optical imaging, and photoluminescence measurements. We also examined the LDS effects of various phosphors on silicon solar cells in terms of optical reflectance and external quantum efficiency. Finally, we examined the LDS effects of the phosphors on photovoltaic performance by measuring photovoltaic current density–voltage characteristics using an air-mass 1.5 global solar simulator. Compared to the control cell, the application of a single phosphor enhanced efficiency by 17.39% (from 11.14% to 13.07%), whereas the application of two different phosphors enhanced efficiency by 31.63% (from 11.14% to 14.66%).

Biological Evaluation and Molecular Docking Studies of Novel 1,3,4-Oxadiazole Derivatives of 4,6-Dimethyl-2-sulfanylpyridine-3-carboxamide

To date, chronic inflammation is involved in most main human pathologies such as cancer, and autoimmune, cardiovascular or neurodegenerative disorders. Studies suggest that different prostanoids, especially prostaglandin E2, and their own synthase (cyclooxygenase enzyme-COX) can promote tumor growth by activating signaling pathways which control cell proliferation, migration, apoptosis, and angiogenesis. Non-steroidal anti-inflammatory drugs (NSAIDs) are used, alongside corticosteroids, to treat inflammatory symptoms particularly in all chronic diseases. However, their toxicity from COX inhibition and the suppression of physiologically important prostaglandins limits their use. Therefore, in continuation of our efforts in the development of potent, safe, non-toxic chemopreventive compounds, we report herein the design, synthesis, biological evaluation of new series of Schiff base-type hybrid compounds containing differently substituted N-acyl hydrazone moieties, 1,3,4-oxadiazole ring, and 4,6-dimethylpyridine core. The anti-COX-1/COX-2, antioxidant and anticancer activities were studied. Schiff base 13, containing 2-bromobenzylidene residue inhibited the activity of both isoenzymes, COX-1 and COX-2 at a lower concentration than standard drugs, and its COX-2/COX-1 selectivity ratio was similar to meloxicam. Furthermore, the results of cytotoxicity assay indicated that all of the tested compounds exhibited potent anti-cancer activity against A549, MCF-7, LoVo, and LoVo/Dx cell lines, compared with piroxicam and meloxicam. Moreover, our experimental study was supported by density functional theory (DFT) and molecular docking to describe the binding mode of new structures to cyclooxygenase.

Using social network analysis to understand multisectoral governance in district-level tobacco control programme implementation in India

IntroductionInterest in multisectoral policies has increased, particularly in the context of low-income and middle-income countries and efforts towards Sustainable Development Goals, with greater attention to understand effective strategies for implementation and governance. The study aimed to explore and map the composition and structure of a multisectoral initiative in tobacco control, identifying key factors engaged in policy implementation and their patterns of relationships in local-level networks in two districts in the state of Karnataka, India.MethodsSocial network analysis (SNA) was used to examine the structure of two district tobacco control networks with differences in compliance with the India’s national tobacco control law. The survey was administered to 108 respondents (n=51 and 57) in two districts, producing three distinct network maps about interaction, information-seeking and decision-making patterns within each district. The network measures of centrality, density, reciprocity, centralisation and E-I index were used to understand and compare across the two districts.ResultsMembers from the department of health, especially those in the District Tobacco Control Cell, were the most frequently consulted actors for information as they led district-level networks. The most common departments engaged beyond health were education, police and municipal. District 1’s network displayed high centralisation, with a district nodal officer who exercised a central role with the highest in-degree centrality. The district also exhibited greater density and reciprocity. District 2 showed a more dispersed pattern, where subdistrict health managers had higher betweenness centrality and acted as brokers in the network.ConclusionCollaboration and cooperation among sectors and departments are essential components of multisectoral policy. SNA provides a mechanism to uncover the nature of relationships and key actors in collaborative dynamics. It can be used as a visual learning tool for policy planners and implementers to understand the structure of actual implementation and concentrate their efforts to improve and enhance collaboration.

Photocontrolled chondrogenic differentiation and long-term tracking of mesenchymal stem cells in vivo by upconversion nanoparticles

Mesenchymal stem cells (MSCs) have multiple differentiation potentials and its clinical application is limited with control cell differentiation and long-term tracing in vivo. Here, we developed a upconversion nanoparticle (UCNP)...

Regulatory Mechanism of Neurotrophin Receptor-Interacting Melanoma Antigen Coding Gene Homolog (NRAGE) Gene Methylation on Apoptosis of Breast Cancer Cell Under Tyrosine Kinases/Methyl Ethyl Ketone/Extracellular Regulated Protein Kinases Signaling Pathway

The aim of this study was to discover the influence of Neurotrophin receptor-interacting MAGE homolog (NRAGE) gene methylation on proliferation (Pro) and apoptosis (Apo) of breast cancer cell (BCC), and its influence on TrkA/MEK/ERK signaling. BCC lines MCF-7, MDA-MB-231, and normal mammary gland cell (MGC) MCF-10 were selected. Expression of NRAGE mRNA and methylation level in cells was analyzed via reverse transcription-polymerase chain reaction (RT-PCR) and methylation-specific PCR. Different concentrations (0, 5, 10 mol/L) of DNA methylase inhibitor 5-aza-2′-deoxycytidine (5-Aza-CdR) were adopted to treat the BCC cell line. With dimethyl sulfoxide (DMSO) treatment as control, cell count, 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, flow cytometry, and Western blot were adopted to detect the Pro, Apo, relative expression (REP) of Apo-related proteins Bcl-2, Bax, and target proteins TrkA, MEK, and ERK1/2 after different treatments. The results showed that NRAGE mRNA level in MDA-MB-231 and MCF-7 was notably reduced versus MCF-10 (P < 0.05), and they could express methylated NRAGE specifically. 5-Aza-CdR can increase unmethylated NRAGE’s expression in BCC. Cell Pro level of the 5 and 10 mol/L treatments was greatly inhibited than DMSO and 0 mol/L treatments (P < 0.05). Apo rate and Apo-related proteins Bcl-2 and Bax increased obviously (P < 0.05). In addition, the phosphorylation levels of TrkA in the 5 and 10 mol/L treatments were considerably reduced (P < 0.05), while that in MEK and ERK1/2 was remarkably increased (P < 0.05). In short, NRAGE methylation can inhibit BCC’s Pro and regulate BCC’s Pro and Apo through TrkA/MEK/ERK signaling.

Rarity of fetal cells in exocervical samples for noninvasive prenatal diagnosis

Objectives The possibility to isolate fetal cells from pregnant women cervical samples has been discussed for five decades but is not currently applied in clinical practice. This study aimed at offering prenatal genetic diagnosis from fetal cells obtained through noninvasive exocervical sampling and immuno-sorted based on expression of HLA-G. Methods We first developed and validated robust protocols for cell detection and isolation on control cell lines expressing (JEG-3) or not (JAR) the HLA-G antigen, a specific marker for extravillous trophoblasts. We then applied these protocols to noninvasive exocervical samples collected from pregnant women between 6 and 14 weeks of gestational age. Sampling was performed through insertion and rotation of a brush at the ectocervix close to the external os of the endocervical canal. Finally, we attempted to detect and quantify trophoblasts in exocervical samples from pregnant women by ddPCR targeting the male SRY locus. Results For immunohistochemistry, a strong specific signal for HLA-G was observed in the positive control cell line and for rare cells in exocervical samples, but only in non-fixative conditions. HLA-G positive cells diluted in HLA-G negative cells were isolated by flow cytometry or magnetic cell sorting. However, no HLA-G positive cells could be recovered from exocervical samples. SRY gene was detected by ddPCR in exocervical samples from male (50%) but also female (27%) pregnancies. Conclusions Our data suggest that trophoblasts are too rarely and inconstantly present in noninvasive exocervical samples to be reliably retrieved by standard immunoisolation techniques and therefore cannot replace the current practice for prenatal screening and diagnosis.

Effect of miR-302b MicroRNA Inhibition on Chicken Primordial Germ Cell Proliferation and Apoptosis Rate

The primordial germ cells (PGCs) are the precursors for both the oocytes and spermatogonia. Recently, a novel culture system was established for chicken PGCs, isolated from embryonic blood. The possibility of PGC long-term cultivation issues a new advance in germ cell preservation, biotechnology, and cell biology. We investigated the consequence of gga-miR-302b-5P (5P), gga-miR-302b-3P (3P) and dual inhibition (5P/3P) in two male and two female chicken PGC lines. In treated and control cell cultures, the cell number was calculated every four hours for three days by the XLS Imaging system. Comparing the cell number of control and treated lines on the first day, we found that male lines had a higher proliferation rate independently from the treatments. Compared to the untreated ones, the proliferation rate and the number of apoptotic cells were considerably reduced at gga-miR-302b-5P inhibition in all PGC lines on the third day of the cultivation. The control PGC lines showed a significantly higher proliferation rate than 3P inhibited lines on Day 3 in all PGC lines. Dual inhibition of gga-miR-302b mature miRNAs caused a slight reduction in proliferation rate, but the number of apoptotic cells increased dramatically. The information gathered by examining the factors affecting cell proliferation of PGCs can lead to new data in stem cell biology.