The interaction between gut microbiota and the host immune system is a complex and understudied field, with cytokines like TNFα, IL-6, IL-8, and IL-10 playing pivotal roles. Commensal bacteria, including lactobacilli, respond to these cytokines through adaptive mechanisms that support their survival and function within the gut. While the influence of cytokines on pathogenic bacteria is well documented, their impact on commensal bacteria, particularly lactobacilli, remains underexplored. This study investigates the transcriptional responses of Lacticaseibacillus rhamnosus strains K32 and R19-3 to various cytokines using next-generation RNA sequencing (RNA-seq). Our findings reveal that cytokines, especially IL-8 and IL-10, significantly alter the L. rhamnosus transcriptome, affecting genes involved in carbohydrate metabolism, stress response, and transcriptional regulation. Notably, IL-8 and IL-10 induce a significant downregulation of genes related to the phosphotransferase system, suggesting a reduction in metabolic activity in response to inflammatory signals. This study unveils a previously unexplored aspect of L. rhamnosus adaptation, highlighting its intricate response to cytokine signals. By modulating gene expression, L. rhamnosus may mitigate the adverse effects of inflammation and promote gut health. These insights could inform the development of targeted probiotic therapies for inflammatory bowel disease (IBD) and other conditions with altered cytokine levels. Our results suggest that co-evolution between a host and gut microbiota enables bacteria to respond to specific cytokines through gene expression changes, revealing a unique and underexplored facet of the interaction between commensal bacteria and the host organism.

Melanoma is an aggressive malignancy with a significant risk of mortality. In recent years, treatment strategies have undergone a paradigm shift with the advent of immunotherapy, particularly immune checkpoint inhibitors (ICIs). Despite notable clinical success, a substantial proportion of patients fail to respond or eventually develop resistance to ICIs. Emerging evidence highlights the gut microbiota as a critical modulator of host immune responses and is one of the potential determinants of immunotherapy efficacy. We performed a cross-cohort analysis of gut microbiome profiles from melanoma patients treated with ICIs. The study integrated the first Russian cohort (62 patients) with six previously published international datasets, comprising a total of 490 patients across seven cohorts. In all cases, metagenomic sequencing was performed using various Illumina platforms, and raw sequencing data were processed using a unified bioinformatic pipeline. Analysis revealed 527 metagenome-assembled genomes (MAGs) significantly associated with treatment outcome: 239 with response and 288 with non-response. Notably, the species Faecalibacterium sp900539945, Phocaeicola vulgatus, Bifidobacterium adolescentis, Faecalibacterium taiwanense, and Gemmiger qucibialis were consistently associated with response, while Enterobacter ludwigii was linked to non-response. Analysis of the Russian cohort revealed both conserved and population-specific microbial signatures, highlighting the coexistence of globally shared and region-dependent microbiome features. Our results also show that species-level annotations may obscure opposing response associations within the same taxa, highlighting the need for MAGs or strain profiling. Together, this study demonstrates that cross-cohort analysis enables the identification of robust and reproducible bacterial markers of immunotherapy response, providing a foundation for microbiome-based prediction and modulation strategies in melanoma.

Cutaneous melanoma is an extremely dangerous tumor disease with poor prognosis at advanced stages. Accounting for a small percentage of all skin tumors, malignant melanoma leads the mortality rate in this group of cancers. Clearly, the search for new drugs and therapeutic approaches for the treatment of cutaneous melanoma is a highly pressing issue in modern medicine. In this study, novel recombinant proteins with anti-melanoma activity, called RGD-apoptins, were produced in an E. coli expression system, and their properties were evaluated in human cell models. These chimeric proteins consist of two parts, each tumor-specific. One part of the chimeric molecule is the RGD peptide, which binds to αVβ3 integrins widely expressed on the surface of malignant melanocytes. The other part is the viral protein apoptin, known to induce programmed cell death in tumor cells but not in normal cells. This molecular design aims to enhance the specificity of potential therapeutic agent toward malignant melanoma cells while reducing cytolytic effects on healthy tissue. In a resazurin assay, RGD-apoptins decreased the viability of MeWo human melanoma cells and did not affect the viability of HaCaT human keratinocyte cell line and primary skin fibroblasts. Using an annexin V assay, we confirmed that malignant melanocytes death occurs via apoptosis. Transcriptomic analysis allowed us to dynamically evaluate the spectrum of differentially expressed genes 24 and 48 h after treating melanoma cells with recombinant RGD-apoptin.

BACKGROUND: Probiotics are capable of modulating immune responses through interactions with the gut microbiota, potentially enhancing the efficacy of immunotherapy and reducing adverse effects of chemotherapy and radiotherapy. Certain probiotic strains have demonstrated the ability to suppress chronic inflammation and augment antitumor immunity; however, their clinical application requires further investigation. AIM: This work aimed to evaluate the effects of oral administration of the probiotic strains Lacticaseibacillus rhamnosus K32 and Bifidobacterium adolescentis 150 on tumor growth and gene expression in the B16-F10 melanoma model, as well as on gut microbiota composition in experimental animals. METHODS: The experiment was conducted in C57BL/6 mice bearing B16-F10 melanoma. Animals were divided into three groups: control (no intervention) and two experimental groups for oral administration of B. adolescentis 150 or L. rhamnosus K32, respectively. Changes in gut microbiota composition were analyzed by full-length 16S rRNA gene sequencing using Oxford Nanopore technology. The transcriptomic response of B16-F10 melanoma cells to probiotic administration was assessed by RNA sequencing. RESULTS: Substantial differences were observed in the effects of the studied probiotic strains on B16-F10 melanoma progression. B. adolescentis 150 significantly stimulated experimental tumor growth by 29% (padj. = 0.02 vs. control; padj. = 0.001 vs. L. rhamnosus K32; adj., Bonferroni correction applied). At the molecular level, this stimulation was associated with suppression of interferon signaling, activation of proliferative pathways (WNT/β-catenin, TGF-β), and reduced expression of immune cell markers in melanoma tissue. In contrast, L. rhamnosus K32 reduced tumor growth by 18% (not significant; padj. = 0.4) and was associated with increased expression of cytotoxic T lymphocyte and NK cell markers, as well as activation of interferon response pathways. Both probiotic strains induced marked alterations in gut microbiota composition, characterized by an increased relative abundance of Klebsiella spp., and were associated with activation of proinflammatory signaling pathways (NF-κB, IL-6/JAK/STAT3, IL-2/STAT5) in tumor tissue. Notably, administration of both probiotics was linked to activation of epithelial–mesenchymal transition and hypoxia in the tumor, potentially creating conditions favorable for tumor progression and metastasis. CONCLUSION: These findings highlight the complex and context-dependent effects of probiotics on tumor development and underscore the need for careful strain selection in the adjuvant therapy of melanoma and other malignancies.

The increasing prevalence of drug-resistant Mycobacteriumtuberculosis (Mtb) and nontuberculous mycobacteria (NTM) underscores the need for novel strategies. Mycobacteriophages are attracting growing interest for therapeutic and diagnostic applications. Here, we describe four new subcluster A3 phages (Cat, Goose1D, Goose1X, and Shep) and investigate their genomic diversity and lytic activity. The phages share >98% nucleotide identity with known A3 members but carry distinct deletions within the lysogeny module: Cat and Goose1X have different repressor-loss variants, and Goose1D lacks the integrase gene, whereas Shep retains an intact module. All phages lysed M. tuberculosis H37Rv, with efficiencies of plating (EOPs) of 10⁻²–10⁻¹, but showed limited activity against NTM. Cat was the most effective against drug-resistant Mtb isolates (EOPs of 10⁻¹–1), remained stable across a broad pH and temperature range, but had a low burst size (8 PFU (plaque-forming units/cell). In lysogeny assays, 6% of Cat-exposed M. smegmatis colonies exhibited a lysogen-like phenotype, but no phage DNA was detected, suggesting spontaneous resistance. Sequencing of one strain revealed an H535Q substitution in the pyruvate carboxylase MSMEG_2412. These findings highlight lysogeny module plasticity in closely related phages and position Cat, with its naturally occurring repressor deletion and potent lytic activity, as a promising candidate against drug-resistant tuberculosis.