Although massive amounts of condition-specific molecular profiles are being accumulated in public repositories every day, meaningful interpretation of these data remains a major challenge. In an effort to identify the biomarkers that describe the key biological phenomena for a given condition, several approaches have been developed over the past few years. However, the majority of these approaches either (i) do not consider the known intermolecular interactions, or (ii) do not integrate molecular data of multiple types (e.g., genomics, transcriptomics, proteomics, epigenomics, etc.), and thus potentially fail to capture the true biological changes responsible for complex diseases (e.g., cancer). In addition, these approaches often ignore the heterogeneity and study bias present in independent molecular cohorts. In this manuscript, we propose a novel multi-cohort and multi-omics meta-analysis framework that overcomes all three limitations mentioned above in order to identify robust molecular subnetworks that capture the key dynamic nature of a given biological condition. Our framework integrates multiple independent gene expression studies, unmatched DNA methylation studies, and protein-protein interactions to identify methylation-driven subnetworks. We demonstrate the proposed framework by constructing subnetworks related to two complex diseases: glioblastoma and low-grade gliomas. We validate the identified subnetworks by showing their ability to predict patients' clinical outcome on multiple independent validation cohorts.

Vietnam is one of the countries most affected worldwide by the highly pathogenic avian influenza (HPAI) virus, which caused enormous economic loss and posed threats to public health. Over nearly two decades, with the antigenic changes in the diversified H5Ny viruses, the limited protective efficacy of the available vaccines was encountered. Therefore, it is necessary to approach a technology platform for the country to accelerate vaccine production that enables quick response to new influenza subtypes. This study utilized a powerful reverse genetics technique to successfully generate a recombinant H5N1 vaccine strain (designated as IBT-RG02) containing two surface proteins (haemagglutinin (HA) and neuraminidase (NA)) from the HPAI H5N1 (A/duck/Vietnam/HT2/2014(H5N1)) of the dominant clade 2.3.2.1c in Vietnam during 2012–2014. Importantly, the IBT-RG02 vaccine candidate has elicited high antibody titres in chickens (geometric mean titre (GMT) of 6.42 and 6.92, log₂ on day 14 and day 28 p.i., respectively). To test the efficacy, immunized chickens were challenged with the circulating virulent strains. As results, there was a high protection rate of 91.6% chickens against the virulent A/DK/VN/Bacninh/NCVD-17A384/2017 of the same clade and a cross-protection of 83.3% against A/duck/TG/NAVET(3)/2013 virus of clade 1.1. Our promising results showed that we can independently master the reverse genetics technology for generation of highly immunogenic vaccine candidates, and henceforth, it is a timely manner to reformulate avian influenza virus vaccines against variable H5 clade HPAI viruses in Vietnam.

Kynurenic acid (KYNA), a small molecule derived from the tryptophan–kynurenine pathway, can readily diffuse across biological membranes and act as an endogenous ligand for receptors such as the aryl hydrocarbon receptor (Ahr). While KYNA dysregulation is implicated in neurodegenerative disorders, the role of the KYNA–Ahr-IL-6 axis in MSC proliferation and differentiation remains poorly defined. We investigated the impact of KYNA on murine bone marrow-derived MSCs (BM-MSCs) at various concentrations (10–200 μM) and time points (8–48 h). The BM-MSC phenotype was assessed via flow cytometry; proliferation, via cell counting; and the gene expression of Ahr, Cyp1a1, Cyp1b1, and Il-6, via quantitative real-time PCR. Multipotency was evaluated through adipogenic, osteogenic, and chondrogenic differentiation assays with histochemical confirmation. KYNA significantly upregulated Ahr mRNA expression. Among the tested concentrations, 100 μM KYNA induced the highest Ahr expression (~19.1 ± 1.5-fold greater than that of the untreated controls, p < 0.005). Notably, 10 and 50 μM KYNA caused moderate induction, whereas compared with 100 μM KYNA, 200 μM did not further increase expression. In addition, KYN treatment increased Cyp1a1, Cyp1b1, and Il-6 expression, with increases of ~64.6 ± 4.5-fold, ~43.6 ± 2.3-fold, and ~41.6 ± 1.2-fold, respectively. Compared with no treatment, 100 µM KYNA enhanced BM-MSC proliferation by 1.210 ± 0.02, 1.189 ± 0.03, and 1.242 ± 0.02-fold across passages P3, P4, and P5, respectively (p < 0.05), without altering Sca-1, CD90, or CD45 expression or impairing trilineage differentiation potential. KYNA may activate the AHR–IL-6 signaling axis to promote BM-MSC expansion. This controlled proliferative effect, without loss of phenotypic or functional integrity, highlights the pharmacological potential of KYNA as a small-molecule modulator for stem cell-based therapies.

The avian influenza virus H5N1 causes the death of millions of avians, including the risk of viral infection in humans. In photodynamic therapy, photosensitizers with light and molecular oxygen might result in the death of cells by generating cytotoxic molecules. Photosensitizers such as methylene blue and laser treatment have been demonstrated to have high efficacy against several types of viruses. The anti-H5N1 effects of several photosensitized compounds, such as methylene blue with laser treatment, are not known. We found that the titer of the ST-2009 virus was 10 × 107 pfu/mL via the MDCK plaque assay. Methylene blue treatment at 0.1 to 1.0 µM had safe effects on MDCK cells. In this study, we demonstrated that the titers of the ST-2009 virus were 3.9 log10 pfu/mL, 5.7 log10 pfu/mL and 6.8 log10 pfu/mL without the methylene blue treatment, but no ST-2009 virus titer was detected after treatment with 0.5 μM methylene blue. In addition, the survival of the ST-2009-infected MDCK cells was significantly greater when the cells were treated with 0.5 to 1.0 μM methylene blue in combination with a laser for 80 s at 16 J/cm2 than in the nontreated control. The survival rates of the MDCK cells were 98.1 ± 0.2 and 96.7 ± 0.4% when the laser treatment (80 s and 16 J/cm2) was combined with 0.5 and 1.0 μM methylene blue, respectively. In addition, without laser treatment or the addition of 0.5 or 1.0 μM methylene blue, the percentages of living cells significantly decreased to 8.3 ± 0.3 and 6.3 ± 0.2%, respectively. The survival of MDCK cells without the addition of methylene blue was 7.5 ± 0.4%, whereas that without laser treatment was 4.6 ± 0.5%. In summary, photosensitizers such as methylene blue with laser treatment can be suitable therapies for the inhibition of avian influenza A virus H5N1.

The hemagglutinin (HA) and neuraminidase (NA) genes were derived from the popular H5N1 virus and the remaining six internal segments were derived from the A/Puerto Rico/8/34 strain (H1N1, PR8). However, some of these candidate strains have been reported to produce relatively low yields in vaccine manufacture does not replicate well in chicken eggs, posing an obstacle to egg-based vaccine production. To address this issue, we explored the possibility that PR8’s hemagglutinin (HA) packaging signals mediate improvement of candidate vaccine virus yield in eggs. We constructed chimeric HA genes having the coding region of IBT-RG02 HA flanked by the 50 packaging signals of PR8’s HA. The growth of candidate vaccine viruses containing the chimeric HA (RG2, RG3, RG4) was increased in embryonated chicken eggs with a nearly 1.5 to 2-fold higher titer than that of control (RG1). It is concluded that the using of chimeric HA fragment can subsequently improve the replication of reversed genetics-derived virus strains in eggs.