Reconstruction and Functional Annotation of P311 Protein-Protein Interaction Network Reveals Its New Functions

Structural variants in the Epb41l4a locus: TAD disruption and Nrep gene misregulation as hypothetical drivers of neurodevelopmental outcomes

Structural variations are a pervasive feature of human genomes, and there is growing recognition of their role in disease development through their impact on spatial chromatin architecture. This understanding has led us to investigate the clinical significance of CNVs in noncoding regions that influence TAD structures. In this study, we focused on the Epb41l4a locus, which contains a highly conserved TAD boundary present in both human chromosome 5 and mouse chromosome 18, and its association with neurodevelopmental phenotypes. Analysis of human data from the DECIPHER database indicates that CNVs within this locus, including both deletions and duplications, are often observed alongside neurological abnormalities, such as dyslexia and intellectual disability, although there is not enough evidence of a direct correlation or causative relationship. To investigate these possible associations, we generated mouse models with deletion and inversion mutations at this locus and carried out RNA-seq analysis to elucidate gene expression changes. We found that modifications in the Epb41l4a TAD boundary led to dysregulation of the Nrep gene, which plays a crucial role in nervous system development. These findings underscore the potential pathogenicity of these CNVs and highlight the crucial role of spatial genome architecture in gene expression regulation.

P311 Promotes IL-4 Receptor‒Mediated M2 Polarization of Macrophages to Enhance Angiogenesis for Efficient Skin Wound Healing

The transition from the proinflammatory phase to the prohealing phase in wound healing is essential for effective skin wound repair, which involves the balance of M1 and M2 polarization of wound-infiltrating macrophages. P311 plays an essential role in promoting wound closure by enhancing the biological function of epidermal stem cells, endothelial cells, and fibroblasts. Nevertheless, whether and how P311 regulates macrophage polarization remains unclear. In this study, we showed that P311 deficiency reduced the M2 polarization of macrophages, thereby attenuating the secretion of M2-like cytokines. The P311 deficiency prolonged the transition from the proinflammatory phase to the prohealing phase, accompanied by weakened angiogenesis and retarded granulation tissue formation, both of which coordinately hinder the healing of skin wounds. Mechanistically, P311 deficiency downregulated the expression of IL-4 receptor on macrophages, followed by less activation of the IL-4 receptor‒signal transducer and activator of transcription 6 signaling pathway, resulting in impaired M2 macrophage polarization. We further revealed that the mTOR signaling pathway was associated with the regulation of P311 on the expression of IL-4 receptor in macrophages. Thus, our study has highlighted the pivotal role of P311 in promoting the M2 polarization of macrophages for effective skin wound healing.

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

BACKGROUND

The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.

METHODOLOGY

We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.

RESULTS

We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).

CONCLUSIONS

There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.

Integrated In-silico Analysis to Study the Role of microRNAs in the Detection of Chronic Kidney Diseases

Background:

MicroRNAs (miRNAs) play an important role in the pathogenesis of various renal diseases, including Chronic Kidney Diseases (CKD). CKD refers to the gradual loss of kidney function with the declining Glomerular Functional Rate (GFR).

Objective:

This study focused on the regulatory mechanism of miRNA to control gene expression in CKD.

Methods:

In this context, two lists of Differentially Expressed Genes (DEGs) were obtained; one from the three selected experiments by setting a cutoff p-value of <0.05 (List A), and one from a list of target genes of miRNAs (List B). Both lists were then compared to get a common dataset of 33 miRNAs, each had a set of DEGs i.e. both up-regulated and down-regulated genes (List C). These data were subjected to functional enrichment analysis, network illustration, and gene homology studies.

Results:

This study confirmed the active participation of various miRNAs i.e. hsa -miR-15a-5p, hsa-miR-195-5p, hsa-miR-365-3p, hsa-miR-30a-5p, hsa-miR-124-3p, hsa-miR-200b-3p, and hsamiR- 429 in the dysregulation of genes involved in kidney development and function. Integrated analyses depicted that miRNAs modulated renal development, homeostasis, various metabolic processes, immune responses, and ion transport activities. Furthermore, homology studies of miRNA-mRNA hybrid highlighted the effect of partial complementary binding pattern on the regulation of genes by miRNA.

Conclusion:

The study highlighted the great values of miRNAs as biomarkers in kidney diseases. In addition, the need for further investigations on miRNA-based studies is also commended in the development of diagnostic, prognostic, and therapeutic tools for renal diseases.

The roles of Qishen granules recipes, Qingre Jiedu, Wenyang Yiqi and Huo Xue, in the treatment of heart failure

ETHNOPHARMACOLOGICAL RELEVANCE

Recipes (Qingre Jiedu (QJ), Wenyang Yiqi (WYYQ) and Huo Xue (HX)) in Qishen granules (QSG) are believed to synergistically exert cardio-protective effects. However, the underlying pattern of each decomposed recipe in QSG and their synergistic effects in the treatment of heart failure (HF) are not clear.

OBJECTIVE

The purpose of this study is to explore the biological contributions of decomposed recipes to therapeutic effects of QSG and reveal the pharmacological mechanism of QSG in treating HF.

MATERIALS AND METHODS

The therapeutic effects of QSG or its recipes on heart failure were examined in wet-lab at both transcription and phenotypic level using HF Sprague-Dawley rats. Sequencing and transcriptome analyses were performed using in silico approaches including identification of differentially expressed genes, pathway enrichment and protein-protein interaction network studies. Specially, an optimized in silico quantitative pathway analysis that maximally extracted gene expression information was developed to reveal differentially expressed pathways (DEPs) among various groups, and is publicly available as R package QPA on GitHub (https://github.com/github-gs/QPA). Finally, the HF-related genes predicted using DEP approach were validated by quantitative real-time polymerase chain reaction and western blot.

RESULTS

Multiple key genes and the associated signaling pathways were shown to be highly relevant for the therapeutic effect of QSG. Decreased expression of Spp1 gene required for inflammatory signaling and profibrotic signaling were observed in failing hearts treated with QJ, WYYQ and HX. Decreased expression of Cx3cr1 gene required for inflammatory signaling was observed in failing hearts treated with WYYQ and HX. Decreased expression of Myc gene required for oxidative stress and Fgfr2 gene required for profibrotic signaling were observed in failing hearts treated with HX and WYYQ, respectively. Increased expression of Adcy1 gene required for cAMP-PKA signaling cascade was observed in failing hearts treated with WYYQ and HX.

CONCLUSIONS

Our study suggests that QJ, WYYQ and HX recipes in QSG achieve synergistic and complementary therapeutic effects through alleviating inflammatory responses, attenuating ventricular remodeling and enhancing myocardial energy supply.