Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset

Microbial community diversity and potential functionality in response to dam construction along the Three Gorge Reservoir, China

River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community.

Pathway-level multi-omics analysis of the molecular mechanisms underlying the toxicity of long-term tacrolimus exposure

Tacrolimus (TAC)-based treatment is associated with nephrotoxicity and hepatotoxicity; however, the underlying molecular mechanisms responsible for this toxicity have not been fully explored. This study elucidated the molecular processes underlying the toxic effects of TAC using an integrative omics approach. Rats were sacrificed after 4 weeks of daily oral TAC administration at a dose of 5 mg/kg. The liver and kidney underwent genome-wide gene expression profiling and untargeted metabolomics assays. Molecular alterations were identified using individual data profiling modalities and further characterized by pathway-level transcriptomics-metabolomics integration analysis. Metabolic disturbances were mainly related to an imbalance in oxidant-antioxidant status, as well as in lipid and amino acid metabolism in the liver and kidney. Gene expression profiles also indicated profound molecular alterations, including in genes associated with a dysregulated immune response, proinflammatory signals, and programmed cell death in the liver and kidney. Joint-pathway analysis indicated that the toxicity of TAC was associated with DNA synthesis disruption, oxidative stress, and cell membrane permeabilization, as well as lipid and glucose metabolism. In conclusion, our pathway-level integration of transcriptome and metabolome and conventional analyses of individual omics profiles, provided a more comprehensive picture of the molecular changes resulting from TAC toxicity. This study also serves as a valuable resource for subsequent investigations aiming to understand the mechanism underlying the molecular toxicology of TAC.

Essential Role of Multi-Omics Approaches in the Study of Retinal Vascular Diseases

Retinal vascular disease is a highly prevalent vision-threatening ocular disease in the global population; however, its exact mechanism remains unclear. The expansion of omics technologies has revolutionized a new medical research methodology that combines multiple omics data derived from the same patients to generate multi-dimensional and multi-evidence-supported holistic inferences, providing unprecedented opportunities to elucidate the information flow of complex multi-factorial diseases. In this review, we summarize the applications of multi-omics technology to further elucidate the pathogenesis and complex molecular mechanisms underlying retinal vascular diseases. Moreover, we proposed multi-omics-based biomarker and therapeutic strategy discovery methodologies to optimize clinical and basic medicinal research approaches to retinal vascular diseases. Finally, the opportunities, current challenges, and future prospects of multi-omics analyses in retinal vascular disease studies are discussed in detail.

Transcriptional Profiles Analysis of COVID-19 and Malaria Patients Reveals Potential Biomarkers in Children

The clinical presentation overlap between malaria and COVID-19 poses special challenges for rapid diagnosis in febrile children. In this study, we collected RNA-seq data of children with malaria and COVID-19 infection from the public databases as raw data in fastq format paired end files. A group of six, five and two biological replicates of malaria, COVID-19 and healthy donors respectively were used for the study. We conducted differential gene expression analysis to visualize differences in the expression profiles. Using edgeR, we explored particularly gene expression levels in different phenotype groups and found that 1084 genes and 2495 genes were differentially expressed in the malaria samples and COVID-19 samples respectively when compared to healthy controls. The highly expressed gene in the COVID-19 group we found CD151 gene which is facilitates in T cell proliferation, while in the malaria group, among the highly expressed gene we identified GBP5 gene which involved in inflammatory response and response to bacterium. By comparing both malaria and COVID-19 infections, the overlap of 62 differentially expressed genes patterns were identified. Among them, three genes (ENSG00000234998, H2AC19 and TXNDC5) were highly upregulated in both infections. Strikingly, we observed 13 genes such as HBQ1, HBM, SLC7A5, SERINC2, ATP6V0C, ST6GALNAC4, RAD23A, PNPLA2, GAS2L1, TMEM86B, SLC6A8, UBALD1, RNF187 were downregulated in children with malaria and uniquely upregulated in children with COVID-19, thus may be further validated as potential biomarkers to delineate COVID-19 from malaria-related febrile infection. The hemoglobin complexes and lipid metabolism biological pathways are highly expressed in both infections. Our study provided new insights for further investigation of the biological pattern in hosts with malaria and COVID-19 coinfection.

Identification of DDX60 as a Regulator of MHC-I Class Molecules in Colorectal Cancer

Immune checkpoint blockade (ICB) therapies induce durable responses in approximately 15% of colorectal cancer (CRC) patients who exhibit microsatellite instability-high (MSI-H) or deficient mismatch repair (dMMR). However, more than 80% of CRC patients do not respond to current immunotherapy. The main challenge with these patients is lack of MHC-I signaling to unmask their cancer cells so the immune cells can detect them. Here, we started by comparing IFNγ signature genes and MHC-I correlated gene lists to determine the potential candidates for MHC-I regulators. Then, the protein expression level of listed potential candidates in normal and cancer tissue was compared to select final candidates with enough disparity between the two types of tissues. ISG15 and DDX60 were further tested by wet-lab experiments. Overexpression of DDX60 upregulated the expression of MHC-I, while knockdown of DDX60 reduced the MHC-I expression in CRC cells. Moreover, DDX60 was downregulated in CRC tissues, and lower levels of DDX60 were associated with a poor prognosis. Our data showed that DDX60 could regulate MHC-I expression in CRC; thus, targeting DDX60 may improve the effects of immunotherapy in some patients.

Diabetic Retinopathy: From Animal Models to Cellular Signaling

Diabetic retinopathy (DR) is an ocular complication of diabetes mellitus (DM), a metabolic disorder characterized by elevation in blood glucose level. The pathogenesis of DR includes vascular, neuronal, and inflammatory components leading to activation of complex cellular molecular signaling. If untreated, the disease can culminate in vision loss that eventually leads to blindness. Animal models mimicking different aspects of DM complications have been developed to study the development and progression of DR. Despite the significant contribution of the developed DR models to discovering the mechanisms of DR and the recent achievements in the research field, the sequence of cellular events in diabetic retinas is still under investigation. Partially, this is due to the complexity of molecular mechanisms, although the lack of availability of models that adequately mimic all the neurovascular pathobiological features observed in patients has also contributed to the delay in determining a precise molecular trigger. In this review, we provide an update on the status of animal models of DR to help investigators choose an appropriate system to validate their hypothesis. We also discuss the key cellular and physiological events of DR in these models.

In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy

Diabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Via RNA-Sequencing, we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 43 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP-PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. While previously considered primarily a vascular disease, attention in DR has shifted to additional mechanisms and cell-types. Our findings offer an unprecedented and unbiased insight into molecular pathways and cell-specific changes in the development of DR, and provide potential avenues for future therapeutic intervention.

Gene expression patterns in synchronized islet populations

In vivo levels of insulin are oscillatory with a period of ~5-10 minutes, indicating that the islets of Langerhans within the pancreas are synchronized. While the synchronizing factors are still under investigation, one result of this behavior is expected to be coordinated and oscillatory intracellular factors, such as intracellular Ca²⁺ levels, throughout the islet population. In other cell types, oscillatory intracellular signals, like intracellular Ca²⁺, have been shown to affect specific gene expression. To test how the gene expression landscape may differ between a synchronized islet population with its reproducible intracellular oscillations and an unsynchronized islet population with heterogeneous oscillations, gene set enrichment analysis (GSEA) was used to compare an islet population that had been synchronized using a glucose wave with a 5-min period, and an unsynchronized islet population. In the population exposed to the glucose wave, 58/62 islets showed synchronization as evidenced by coordinated intracellular Ca²⁺ oscillations with an average oscillation period of 5.1 min, while in the unsynchronized population 29/62 islets showed slow oscillations with an average period of 5.2 min. The synchronized islets also had a significantly smaller drift of their oscillation period during the experiment as compared to the unsynchronized population. GSEA indicated that the synchronized population had reduced expression of gene sets related to protein translation, protein turnover, energy expenditure, and insulin synthesis, while those that were related to maintenance of cell morphology were increased.

Differential gene expression profiling of the sciatic nerve in type 1 and type 2 diabetic mice

Diabetic peripheral neuropathy (DPN) is a common complication of diabetes mellitus (DM). The pathogenic mechanisms of DPN and the therapeutic interventions required may be distinct between type 1 (T1) and type 2 (T2) DM. However, the molecular mechanisms underlying the pathogenesis of DPN in both types of diabetes remain unclear. The aim of the current study was to identify the changes in genes and pathways associated with DPN in sciatic nerves of T1- and T2DM mice using bioinformatics analysis. The microarray profiles of sciatic nerves of T1DM (GSE11343) and T2DM (GSE27382) mouse models were downloaded from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) in each. DEGs in the two types of DM (with fold change ≥2 and P<0.05) were identified with BRB-ArrayTools. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins and visualized using Cytoscape. Compared with control samples, 623 and 1,890 DEGs were identified in sciatic nerves of T1- and T2DM mice, respectively. Of these, 75 genes were coordinately dysregulated in the sciatic nerves of both models. Many DEGs unique to T1DM mice were localized to the nucleoplasm and were associated with regulation of transcription processes, while many unique to T2DM mice were localized at cell junctions and were associated with ion transport. In addition, certain DEGs may be associated with the different treatment strategies used for the two types of DM. This analysis provides insight into the functional gene sets and pathways operating in sciatic nerves in T1- and T2DM. The results should improve understanding of the molecular mechanisms underlying the pathophysiology of DPN, and provide information for the development of therapeutic strategies for DPN specific to each type of DM.

Nogo receptor knockdown and ciliary neurotrophic factor attenuate diabetic retinopathy in streptozotocin-induced diabetic rats

Diabetic retinopathy (DR) is a common complication of diabetes mellitus (DM). We investigated whether Nogo receptor (NgR) knockdown and ciliary neurotrophic factor (CNTF) treatment, either alone or in combination, ameliorated diabetic retinopathy (DR) in diabetic rat model. STZ‑induced diabetic rats were administrated for a total of 12 weeks with 3 µM siRNA (5 µl) once every 6 weeks and/or 1 µg CNTF weekly. The retinal tissues were excised. We measured cell number in ganglion cell layer (GCL) using H&E staining and cell apoptosis using TUNEL assay. Bax, Bcl‑2, Caspase‑3, F‑actin, GAP‑43, NgR, RhoA and Rock1 levels were then analyzed by Western blotting, Immunohistochemistry or Real‑time PCR. We found that NgR siRNA or CNTF injection alone significantly increased cell count in GCL in diabetic rats, inhibited ganglion cell apoptosis, elevated Bcl‑2, F‑actin and GAP‑43, and decreased Bax, Caspase‑3, NgR, RhoA and Rock1 levels. Combination treatment further prevented retinal ganglion cell loss, enhanced growth cone cytoskeleton and axonal regeneration, and suppressed NgR/RhoA/Rock1. Our results indicate that combination therapy has therapeutic potential for the treatment of DR.