Identification of joint gene players implicated in the pathogenesis of HTLV-1 and BLV through a comprehensive system biology analysis

Comprehensive analysis of the miRNA-mRNA regulatory network involved in spontaneous recovery of an H2O2-induced zebrafish cataract model

OBJECTIVE

To identify the hub miRNAs and mRNAs contributing to the spontaneous recovery of an H2O2-induced zebrafish cataract model.

METHODS

Zebrafishes were divided into three groups, i.e., Group A, which included normal control fish (day 0), and Groups B and C, where fish were injected with 2.5% hydrogen peroxide into the anterior chamber and reared for 14 and 30 days, respectively. Fish eyes were examined by stereomicroscope photography and optical coherence tomography (OCT). RNA profiles of fish lenses were detected by RNA sequencing. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified among three groups. The DEGs and DEmiRs, which changed in opposite positions between "B vs. A" and "C vs. B" were defined as ODGs (opposite positions changed DEGs) and ODmiRs (opposite positions changed DEmiRs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis were carried out by R language. The protein-protein interaction network (PPI) was constructed using STRING. Potential targets of miRNAs were obtained using miRanda. miRNA-mRNA networks were constructed by Cytoscape.

RESULTS

The fish lens opacity formed on day 14 and recovered to transparent on day 30 after injection. Compared to group B, 1366 DEGs and 54 DEmiRs were identified in group C. "C vs. B" DEGs were enriched in gene clusters related to development and oxidative phosphorylation. Target genes of DEmiRs were enriched in clusters such as development and cysteine metabolism. Among three groups, 786 ODGs and 27 ODmiRs were identified, and 480 ODGs were predicted as targets of ODmiRs. Target ODGs were enriched in pathways related to methionine metabolism, ubiquitin, sensory system development, and structural constituents of the eye lens. In addition, we established an ODmiRs-ODGs regulation network.

CONCLUSION

We identified several hub mRNAs and altered miRNAs in the formation and reversal of zebrafish cataracts. These hub miRNAs/mRNAs could be potential targets for the non-surgical treatment of ARC.

Key candidate genes and pathways in T lymphoblastic leukemia/lymphoma identified by bioinformatics and serological analyses

T-cell acute lymphoblastic leukemia (T-ALL)/T-cell lymphoblastic lymphoma (T-LBL) is an uncommon but highly aggressive hematological malignancy. It has high recurrence and mortality rates and is challenging to treat. This study conducted bioinformatics analyses, compared genetic expression profiles of healthy controls with patients having T-ALL/T-LBL, and verified the results through serological indicators. Data were acquired from the GSE48558 dataset from Gene Expression Omnibus (GEO). T-ALL patients and normal T cells-related differentially expressed genes (DEGs) were investigated using the online analysis tool GEO2R in GEO, identifying 78 upregulated and 130 downregulated genes. Gene Ontology (GO) and protein-protein interaction (PPI) network analyses of the top 10 DEGs showed enrichment in pathways linked to abnormal mitotic cell cycles, chromosomal instability, dysfunction of inflammatory mediators, and functional defects in T-cells, natural killer (NK) cells, and immune checkpoints. The DEGs were then validated by examining blood indices in samples obtained from patients, comparing the T-ALL/T-LBL group with the control group. Significant differences were observed in the levels of various blood components between T-ALL and T-LBL patients. These components include neutrophils, lymphocyte percentage, hemoglobin (HGB), total protein, globulin, erythropoietin (EPO) levels, thrombin time (TT), D-dimer (DD), and C-reactive protein (CRP). Additionally, there were significant differences in peripheral blood leukocyte count, absolute lymphocyte count, creatinine, cholesterol, low-density lipoprotein, folate, and thrombin times. The genes and pathways associated with T-LBL/T-ALL were identified, and peripheral blood HGB, EPO, TT, DD, and CRP were key molecular markers. This will assist the diagnosis of T-ALL/T-LBL, with applications for differential diagnosis, treatment, and prognosis.

Virus-Host Protein Interaction Network of the Hepatitis E Virus ORF2-4 by Mammalian Two-Hybrid Assays

Throughout their life cycle, viruses interact with cellular host factors, thereby influencing propagation, host range, cell tropism and pathogenesis. The hepatitis E virus (HEV) is an underestimated RNA virus in which knowledge of the virus-host interaction network to date is limited. Here, two related high-throughput mammalian two-hybrid approaches (MAPPIT and KISS) were used to screen for HEV-interacting host proteins. Promising hits were examined on protein function, involved pathway(s), and their relation to other viruses. We identified 37 ORF2 hits, 187 for ORF3 and 91 for ORF4. Several hits had functions in the life cycle of distinct viruses. We focused on SHARPIN and RNF5 as candidate hits for ORF3, as they are involved in the RLR-MAVS pathway and interferon (IFN) induction during viral infections. Knocking out (KO) SHARPIN and RNF5 resulted in a different IFN response upon ORF3 transfection, compared to wild-type cells. Moreover, infection was increased in SHARPIN KO cells and decreased in RNF5 KO cells. In conclusion, MAPPIT and KISS are valuable tools to study virus-host interactions, providing insights into the poorly understood HEV life cycle. We further provide evidence for two identified hits as new host factors in the HEV life cycle.

Pathogenicity and virulence of human T lymphotropic virus type-1 (HTLV-1) in oncogenesis: adult T-cell leukemia/lymphoma (ATLL)

Adult T-cell leukemia/lymphoma (ATLL) is an aggressive malignancy of CD4⁺ T lymphocytes caused by human T lymphotropic virus type-1 (HTLV-1) infection. HTLV-1 was brought to the World Health Organization (WHO) and researchers to address its impact on global public health, oncogenicity, and deterioration of the host immune system toward autoimmunity. In a minority of the infected population (3-5%), it can induce inflammatory networks toward HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), or hijacking the infected CD4⁺ T lymphocytes into T regulatory subpopulation, stimulating anti-inflammatory signaling networks, and prompting ATLL development. This review critically discusses the complex signaling networks in ATLL pathogenesis during virus-host interactions for better interpretation of oncogenicity and introduces the main candidates in the pathogenesis of ATLL. At least two viral factors, HTLV-1 trans-activator protein (TAX) and HTLV-1 basic leucine zipper factor (HBZ), are implicated in ATLL manifestation, interacting with host responses and deregulating cell signaling in favor of infected cell survival and virus dissemination. Such molecules can be used as potential novel biomarkers for ATLL prognosis or targets for therapy. Moreover, the challenging aspects of HTLV-1 oncogenesis introduced in this review could open new venues for further studies on acute leukemia pathogenesis. These features can aid in the discovery of effective immunotherapies when reversing the gene expression profile toward appropriate immune responses gradually becomes attainable.

Molecular insight into the study of adult T-cell leukemia/lymphoma (ATLL): Ten-year studies on HTLV-1 associated diseases in an endemic region

The outcome of successful infection, including human T-cell leukemia virus type 1 (HTLV-1), is determined by the interactions between the host and the infectious agent. Ten years of work on HTLV-1-associated diseases in an endemic region of Iran have been critically compared in the present study. The outstanding findings of RNA-seq, system biology analysis, and gene expression measurements on adult T-cell leukemia/lymphoma (ATLL) and enzootic bovine leukosis(EBL) in our lab encouraged us to investigate the significant role of oncogenes in the ATLL malignancy. Most studies assessed such interactions by the proviral load (PVL), Tax, and HBZ regulatory proteins in HTLV-1 and the host's immunological and cell cycle factors. The current study is a comprehensive comparing view of our previously published and unpublished results investigating the HTLV-1-host interactions leading to the transformation of the infected cell. The main focus has been on the essential proteins implicated in the virus dissemination, cell survival, and proliferation of infected cells toward leukemia development and progression. Similar to its homolog BLV-AS-1-2 in EBL, the HTLV-1-HBZ is a pivotal factor in the maintenance and progression of the ATLL. In addition, the inappropriate activities of the PI3K/Akt pathway, BRCAs, and RAD51 in the DNA repair system, which are orchestrating many other immortalization pathways, might be the central factors in the manifestation of ATLL. HTLV-1-HBZ and the host PI3K/Akt pathway, BCAs, and RAD51 could be suggested as influential targets for the prognosis and proper therapy of ATLL.

Identification of the circRNA-miRNA-mRNA Regulatory Network in Pterygium-Associated Conjunctival Epithelium

To investigate the regulatory mechanism of pterygium formation, we detected differentially expressed messenger RNAs (DE-mRNAs) and differentially expressed circular RNAs (DE-circRNAs) in pterygium-associated conjunctival epithelium (PCE) and normal conjunctival epithelium (NCE). Genome-wide mRNA and circRNA expression profiles of PCE and NCE were determined using high-throughput sequencing. Bioinformatics analyses, including Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) analysis, were conducted. The microRNAs (miRNAs) interacting with the hub DE-mRNAs and DE-circRNAs were predicted and verified using real-time quantitative PCR (RT-qPCR). The data showed that there were 536 DE-mRNAs (280 upregulated and 256 downregulated mRNAs) and 78 DE-circRNAs (20 upregulated and 58 downregulated circRNAs) in PCE. KEGG enrichment analysis indicated that the DE-mRNAs were mainly involved in the following biological processes: IL-17 signalling pathway, viral protein interaction with cytokine and cytokine receptor, cytokine-cytokine receptor interaction, ECM-receptor interaction, and focal adhesion. The GSEA results revealed that the epithelial mesenchymal transition (EMT) process was significantly enriched in upregulated mRNAs. The pterygium-associated circRNA-miRNA-mRNA network was established based on the top 10 DE-circRNAs, 4 validated miRNAs (upregulated miR-376a-5p and miR-208a-5p,downregulated miR-203a-3p and miR-200b-3p), and 31 DE-mRNAs. We found that miR-200b-3p, as a regulator of FN1, SDC2, and MEX3D, could be regulated by 5 upregulated circRNAs. In addition, we screened out EMT-related DE-mRNAs, including 6 upregulated DE-mRNAs and 6 downregulated DE-mRNAs. The EMT-related circRNA-miRNA-mRNA network was established with the top 10 circRNAs, 8 validated miRNAs (upregulated miR-17-5p, miR-181a-5p, and miR-106a-5p, downregulated miR-124-3p, miR-9-5p, miR-130b-5p, miR-1-3p, and miR-26b-5P), and 12 EMT-related DE-mRNAs. We found that hsa_circ_0002406 might upregulate FN1 and ADAM12 by sponging miR-26b-5p and miR-1-3p, respectively, thus promoting EMT in pterygium. Briefly, the study provides a novel viewpoint on the molecular pathological mechanisms in pterygium formation. CircRNA-miRNA-mRNA regulatory networks participate in the pathogenesis of pterygium and might become promising targets for pterygium prevention and treatment.

Cuproptosis-related gene signature correlates with the tumor immune features and predicts the prognosis of early-stage lung adenocarcinoma patients

Background: Although a majority of early-stage lung adenocarcinoma (es-LUAD) patients have a favorable prognosis, there are still some cases with a risk of recurrence and metastasis. Cuproptosis is a new form of death that differs from other programmed cell death. However, no study has been reported for setting a prognostic model of es-LUAD using cuproptosis pattern-related genes.

Methods: Using multiple R packages, the data from the GEO database was processed, and es-LUAD patients was classified into two patterns based on cuproptosis-related genes. Key differentially expressed genes (DEGs) in the two patterns were screened to construct a prognostic signature to assess differences in biological processes and immunotherapy responses in es-LUAD. Tumor microenvironment (TME) in es-LUAD was analyzed using algorithms such as TIMER and ssGSEA. Then, a more accurate nomogram was constructed by combining risk scores with clinical factors.

Results: Functional enrichment analysis revealed that DEGs in two patterns were correlated with organelle fission, nuclear division, chromosome segregation, and cycle-related pathways. Univariate Cox regression and Lasso-Cox regression analyses identified six prognostic genes: ASPM, CCNB2, CDC45, CHEK1, NCAPG, and SPAG5. Based on the constructed model, we found that the high-risk group patients had higher expression of immune checkpoints (CTLA4, LAG3, PD-L1, TIGIT and TIM3), and a lower abundance of immune cells. Lastly, the nomogram was highly accurate in predicting the 1-, 3-, and 5-year survival status of patients with es-LUAD based on risk scores and clinical factors.

Conclusion: The cuproptosis pattern-related signature can serve as a potential marker for clinical decision-making. It has huge potential in the future to guide the frequency of follow-up and adjuvant therapy for es-LUAD patients.

Identifying RBBP7 as a Promising Diagnostic Biomarker for BK Virus-Associated Nephropathy

BK virus-associated nephropathy (BKVN) remains a major infectious complication due to powerful immunosuppression in kidney transplant recipients, and its histologic appearance can mimic rejection, leading to diagnostic and treatment dilemmas thus molecular diagnostic methods would be beneficial. We collected gene expression profiles of 169 kidney biopsies taken from BKVN, rejection, and stable functioning allografts, based on single sample gene set enrichment analysis and random forest algorithm, and three hallmark activities associated with DNA damage and proliferation were found to be relatively specific in BKVN. Subsequently, weighted gene co-expression network analysis and support vector machines (SVM) algorithm identified RBBP7 as a robust and promising biomarker with high accuracy in both training and validation cohorts (AUC =0.938, 0.977, respectively). Besides, potential drugs for BKVN treatment such as mepacrine were discovered, which may contribute to targeted antiviral therapy and effective patient management rather than simply reducing the doses of immunosuppressive agents in clinical practice. RBBP7 (retinoblastoma binding protein 7) serves as component of serval complexes that regulate chromatin metabolism and functions in affecting DNA replication and controlling cell proliferation. In this research, upregulation of RBBP7 was found to be associated with the higher infiltration of CD8 naïve T, iTreg, and neutrophil cells and the lower amounts of Th1, central memory T, NKT, CD8 T, and dendritic cells. Moreover, the infiltration of Th1, Th17, and NKT cells was steadily different between BKVN and rejection allografts through immune cell assessment. In conclusion, we identified and verified RBBP7 as a molecular biomarker for BKVN diagnosis, which demonstrated great distinguishing ability with allograft rejection and would support clinical decision-making.

Transcriptome analysis to reveal the mechanism of the effect of Echinops latifolius polysaccharide B on palmitate-induced insulin-resistant

Hepatic insulin resistance is a crucial pathological process in type 2 diabetes mellitus (T2DM) associated with visceral adiposity and metabolic disorders. Echinops latifolius polysaccharide B (ETPB), a polysaccharide extracted from Echinops latifolius Tausch, increases insulin sensitivity in the high-fat diet-fed and STZ induced SD rat model and even prevented hepatic metabolic disorders. However, the mechanism by which ETPB improves carbohydrate and lipid metabolisms in the liver with insulin resistance remains largely unknown. In the present work, an lnsulin resistance cell model (IR-HepG2) was established. Glucose consumption, glycogen content, triglycerides (TG), and free fatty acids (FFAs) levels were detected. The result revealed that the intervention of ETPB significantly increased glucose consumption and glycogen synthesis and reduced FFAs and TG production in IR-HepG2 cells. Further, we also employed RNA-seq to identify differentially expressed miRNAs (DEMs) and mRNAs (DEGs) with a fold change of ≥ 1.5 and p-value of <0.05. Finally, we identified 1028, 682, 382, 1614, 519 and 825 DEGs, and 71, 113, 94, 68, 52 and 38 DEMs in different comparisons, respectively. Based on a short time-series expression miner (STEM) analysis, six profiles were chosen for further analysis. Seventeen insulin resistance-associated dynamic DEGs were identified during ETPB stimulation. Based on these dynamic DEGs, the related miRNAs were acquired from DEMs, and an integrated miRNA-mRNA regulatory network was subsequently constructed. Besides, some DEGs and DEMs were validated using qPCR. This study provides transcriptomic evidence of the molecular mechanism involved in HepG2 insulin resistance, leading to the discovery of miRNA-based target therapies for ETPB.