Search Results (11,899)

Background: Long noncoding RNAs (lncRNAs) have emerged as critical regulators of hepatic metabolism and disease progression. The hepatocyte nuclear factor 1 alpha antisense 1 (HNF1A-AS1) lncRNA modulates liver-specific transcription factors; however, its physiological role in diet-dependent lipid homeostasis remains poorly defined. Methods: In this study, we investigated the mouse ortholog, Hnf1a opposite strand 1 (Hnf1aos1), using AAV-mediated knockdown in C57BL/6J mice fed either a chow diet (10% kcal from fat) or a high-fat diet (HFD; 60% kcal from fat) for 12 weeks. Metabolic phenotyping included hepatic lipid quantification, histological analysis, serum biochemistry, and quantitative gene expression profiling. Results: Loss of Hnf1aos1 produced distinct, diet-dependent alterations in hepatic lipid handling. Under chow conditions, knockdown mice exhibited selective hepatic cholesterol accumulation (6.10 ± 2.9 mg/g tissue vs. 3.51 ± 1.1 mg/g in controls), accompanied by dysregulation of cholesterol clearance pathways. In contrast, under HFD conditions, knockdown precipitated severe macrovesicular degeneration, with hepatic triglyceride levels approximately doubled relative to HFD-fed controls (51.72 ± 19.8 mg/g vs. 26.34 ± 11.9 mg/g) and a numerically elevated triglyceride-to-cholesterol ratio (TG:TC ≈ 6.1:1; p = 0.0621, trend). Chow/Kd mice gained significantly less weight than chow-fed controls, whereas HFD/Kd mice exhibited weight gain comparable to HFD controls despite severe hepatic steatosis. This paradoxical phenotype suggests impaired metabolic feedback at the post-transcriptional level, in which compensatory upregulation of Hnf1a mRNA is insufficient to suppress lipid-associated genes such as Cd36, despite profound lipid overload; however, HNF1A protein levels were not directly measured in this study. Conclusion: Collectively, these findings identify Hnf1aos1 as a regulator of hepatic lipid homeostasis whose loss produces a phenotype consistent with inappropriate lipid accumulation during nutrient excess, without defining the underlying molecular mechanism. Our results support a role for Hnf1aos1 in shaping hepatic metabolic plasticity and provide insight into lncRNA-associated MASLD phenotypes. Full article

Wolbachia is an obligate endosymbiotic alphaproteobacterium that is widely distributed among insects. It also infects the European orthopteran Chorthippus parallelus parallelus (Cpp). In this subspecies, Wolbachia induces a reproductive barrier through uni- and bidirectional cytoplasmic incompatibilities. Recently, we found that it also modifies the expression of genes related to essential physiological pathways in Cpp. Here, we have analysed the influence of Wolbachia infection on the epigenetic profiles in Cpp gonads of infected and uninfected males and females, since they constitute Wolbachia’s main target. We characterised de novo nine genes related to epigenetic mechanisms and their transcriptional activity, together with global DNA methylation levels. The results indicate that Wolbachia influences the epigenetic mechanisms in Cpp mainly in females, inducing the expression of genes related to histone deacetylation and reducing the global DNA methylation percentage. This study provides the first evidence of Wolbachia’s ability to alter epigenetic processes in Cpp, increasing our understanding of this symbiotic relationship, with potential implications for the induced reproductive isolation within and between subspecies of C. parallelus. It also offers new insights into the molecular basis of host–symbiont biology in a group for which this information is rather scarce. Full article

Nuclear factor kappa B (NF-κB) signaling plays a central role in inflammation, immunity, cell survival, and cancer progression. Its constitutive activation is frequently observed in breast cancer, contributing to tumor growth, treatment resistance, and metastasis. MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression and may modulate NF-κB signaling in a subtype-specific or -independent manner. The aim of the study was to identify miRNAs that may potentially regulate the activity of genes associated with NF-κB signaling across five molecular subtypes of breast cancer in Polish women. Tumor and matched normal tissue samples were collected from 405 patients with five breast cancer subtypes: luminal A (n = 130), HER2-negative luminal B (n = 100), HER2-positive luminal B (n = 96), non-luminal HER2-positive (n = 36), and triple-negative breast cancer (TNBC, n = 43). Expression profile of selected NF-κB-related genes were evaluated using mRNA microarrays and RT-qPCR. Protein levels were assessed by ELISA. Candidate regulatory miRNAs were identified via miRNA microarrays and validated using the miRDB database. A consistent upregulation of MAP3K7, TAB2, TNFAIP3, CSNK2A1, BCL2L1, XIAP, CXCL2, and PLAU was observed across all subtypes, suggesting activation of canonical NF-κB signaling. Downregulation of specific miRNAs, miR-1297 and miR-30a (targeting MAP3K7), miR-134 (TAB2), miR-125b (TNFAIP3), and miR-4329 (XIAP), may contribute to this deregulation. For CSNK2A1, BCL2L1, CXCL2, and PLAU, no regulatory miRNAs meeting our criteria were identified. Our study reveals a subtype-independent activation of the canonical NF-κB signaling pathway in breast cancer, underpinned by consistent upregulation of key components (at both the transcript and protein levels. Dysregulation of specific miRNAs likely contributes to this altered gene expression. These findings suggest the presence of a common NF-κB-driven oncogenic program across molecular subtypes, with potential implications for developing miRNA-based therapeutic strategies targeting inflammation, survival signaling, and treatment resistance in breast cancer. Full article

Banana productivity is severely limited by drought, yet the molecular basis of drought adaptation and endophyte-mediated stress alleviation remains poorly understood. Here, we performed a genome-wide analysis of the SQUAMOSA promoter-binding protein-like (SPL) transcription factor family in Musa acuminata and examined their transcriptional responses to drought stress and Serendipita indica inoculation. We identified 38 MaSPL genes, all encoding proteins with the conserved SBP domain and predicted nuclear localization. Phylogenetic, motif, gene structure, and collinearity analyses indicated that MaSPL genes are evolutionarily conserved, unevenly distributed across chromosomes, and expanded primarily through segmental duplication under purifying selection. Promoter analysis showed several cis-acting elements and transcription factor binding sites related to light, phytohormone, and stress signaling. Ten MaSPL genes were predicted as putative targets of miR156. qRT-PCR analysis showed that drought stress markedly downregulated the tested MaSPL genes, whereas miR156a expression increased, supporting an inverse regulatory relationship. Under drought, S. indica inoculation enhanced expression of most tested MaSPLs, restoring transcript accumulation while reducing miR156a to near-basal levels. Notable responses were observed in members of the MaSPL2, MaSPL9, and MaSPL13, respectively. S. indica improves drought tolerance by enhancing antioxidant defenses, reducing oxidative stress, and preserving photosynthetic and osmotic stability. Taken together, our results demonstrate that S. indica confers drought resilience in banana by counteracting drought-induced repression of MaSPL genes via the miR156–SPL module and by strengthening key physiological defense mechanisms. Full article

Uridine diphosphate glucuronosyltransferases (UGTs) are critical phase II detoxification enzymes; however, their mutational landscape and protective roles against chemical carcinogenesis in hepatocellular carcinoma (HCC) remain poorly defined. Here, targeted sequencing of ten liver-enriched UGT genes in 38 paired tissues from a Chinese HCC cohort revealed striking mutation frequencies in UGT2B15 (44.74%), UGT2B10 (36.84%), and UGT2B17 (26.32%). This genomic instability was accompanied by a profound downregulation of UGT2B15 mRNA (9.02-fold decrease, p < 0.001) and protein levels (Z-score = 2.32, p = 0.0093) in tumors, with higher UGT2B15 expression correlating with improved overall survival in TCGA cohorts (HR = 1.724, p = 0.012). Mechanistically, we identified the androgen receptor (AR) as a direct transcriptional regulator of UGT2B15 and UGT2B17, with dihydrotestosterone (DHT) inducing dose-dependent increases in their expression, thereby linking endocrine signaling to hepatic detoxification. Transcriptomic profiling following UGT2B15 knockdown in HCC cells revealed a significant enrichment in chemical carcinogenesis-related pathways. Crucially, UGT2B15 deficiency severely exacerbated carbon tetrachloride (CCl₄)- and ethanol-induced hepatotoxicity both in vitro and in vivo. Our study uncovers a profound impairment of UGT-mediated detoxification in HCC and establishes the AR–UGT2B15 axis as a critical barrier against chemical-induced liver injury, highlighting its potential as a chemopreventive target in carcinogen-exposed populations. Full article

Objective: Gastric cancer (GC) is characterized by molecular heterogeneity, yet current classifications are largely based on cross-sectional molecular profiles and do not account for the temporal order of mutation accumulation. This study aimed to reconstruct somatic mutation trajectories to identify prognostically distinct subtypes and to examine transcriptomic and microenvironmental features associated with these inferred trajectories. Methods: We applied the Subtype and Stage Inference (SuStaIn) algorithm to TCGA-STAD somatic mutation data to infer the temporal sequence of mutation accumulation. Stage-correlated gene expression analysis was performed to identify genes whose expression levels changed with evolutionary stage. The tumor microenvironment (TME) was characterized using EcoTyper and single-cell RNA sequencing deconvolution, while drug sensitivity was estimated through transcriptome-based IC₅₀ prediction. The clinical relevance of the inferred trajectories was further evaluated in three independent external transcriptomic cohorts. Results: We identified two distinct evolutionary trajectories: the Accelerated Path (AP, 65%) and the Gradual Path (GP, 35%). In the AP, TP53 mutations were positioned at an earlier evolutionary stage (Stage 3) compared to the GP (Stage 8). AP patients had significantly worse overall survival (Hazard Ratio = 1.437, p = 0.044, adjusted for clinical stage and molecular subtypes). The AP was associated with stage-correlated downregulation of the sodium channel gene SCN4A (ρ = −0.36, p < 0.001) and an increase in a squamous-associated gene expression score, while the GP showed stage-correlated expression changes in the mitochondrial gene SDHD (ρ = −0.35, p < 0.001). The AP was further characterized by higher inferred abundance of extracellular matrix CAFs (eCAFs) and lower inferred immune cell scores, whereas the GP was associated with higher inferred signatures of activated B cells and effector memory T cells. Computational drug sensitivity modeling predicted a negative correlation between AP stage and IC₅₀ values for 5-Fluorouracil and Docetaxel. Conclusions: Two distinct mutational ordering patterns identified by SuStaIn are associated with divergent transcriptomic features, TME compositions, and clinical outcomes in gastric cancer. The AP subtype is characterized by early TP53 mutations, SCN4A downregulation, and a stromal-enriched microenvironment, while the GP subtype is associated with later TP53 mutations, SDHD-correlated expression, and higher inferred immune cell scores. The reproducibility of these associations was confirmed in independent cohorts. The computational drug sensitivity predictions and the proposed mechanistic links between gene expression patterns and clinical outcomes should be viewed as hypothesis-generating findings that require prospective and functional validation. Full article

Difficult-to-treat systemic lupus erythematosus (D2T-SLE) remains a major unmet challenge in contemporary lupus care, yet it continues to be defined predominantly by clinical non-response rather than underlying biology. Current biomarkers largely quantify inflammatory burden, immune complex activity, or organ damage and do not reliably capture persistent activation of pathogenic pathways under therapy. Emerging multi-omics, single-cell, and longitudinal studies suggest that, in a subset of patients, apparent treatment failure may reflect incomplete attenuation of dominant immune circuits rather than uniformly elevated inflammation. We propose molecular refractoriness in systemic lupus erythematosus (SLE) as sustained, pathway-level immune activity despite apparently adequate, mechanism-directed therapy. We outline the major immune programs implicated in this process—including interferon-enriched, B-cell/plasmablast-associated, neutrophil extracellular trap (NET)-related, cytotoxic T-cell, and cytokine-associated states—and discuss their relevance for biomarker development and precision trial design. Importantly, we emphasize that interferon gene signatures (IGS) should be interpreted as context-dependent and non-specific markers of interferon responsiveness, reflecting combined activity of type I, II, and III interferons, and functioning primarily as predictive rather than mechanistic biomarkers. We further highlight critical limitations of a purely endotype-based model, including the need to distinguish true molecular refractoriness from damage-dominant and pseudo-refractory states, as well as the emerging role of immune-reset strategies such as cluster of differentiation 19 (CD19)-directed chimeric antigen receptor T-cell (CAR-T) therapy, which may overcome refractoriness independently of specific pathway dominance. These observations suggest that difficult-to-treat SLE encompasses biologically heterogeneous states that may not be fully captured by pathway-resolved stratification alone. Reframing D2T-SLE as a biologically heterogeneous state of incomplete immune attenuation may help bridge the gap between clinical treatment failure and mechanism-informed precision medicine in systemic lupus erythematosus. Full article

Sugars play a pivotal regulatory role in floral bud dormancy release in Prunus mume, a process that critically determines subsequent flowering time. However, the precise molecular mechanisms linking sugar metabolism to this developmental transition remain poorly understood. To address this gap, we integrated physiological profiling and transcriptomic sequencing using two cultivars with contrasting flowering phenologies: the early-flowering ‘Chaotang Gongfen’ (CTGF) and the late-flowering ‘Shichu Jin’ (SCJ). Exogenous sugar treatments were applied separately to floral buds of the cultivar ‘Yilian’ to evaluate the effect of sugars on dormancy release. During dormancy release, glucose and sucrose contents increased progressively and showed significant positive correlations with bud break rates in both CTGF and SCJ (r > 0.75). Consistently, exogenous application of glucose and sucrose significantly accelerated bud break in ‘Yilian’, whereas mannose exhibited an inhibitory effect. Transcriptome analysis of CTGF and SCJ revealed significant enrichment of starch and sucrose metabolism, hormone signal transduction, and stress-responsive pathways. Key metabolic genes, notably the α-amylase gene PmAMY1-2 and the cell wall invertase genes PmCWINV1/4, were upregulated during this transition. Weighted gene co-expression network analysis (WGCNA) further identified PmFRK4, PmSUS6, and the aforementioned invertases as candidate genes within a sugar-associated regulatory module. Collectively, these findings support a model in which glucose and sucrose accumulation promotes endodormancy release via the transcriptional activation of starch and sucrose catabolic pathways. This study provides a theoretical framework for deciphering dormancy regulation in woody perennials and offers potential targets for the precise manipulation of flowering time. Full article

To investigate the response mechanism of cold-resistant Enshi black pig breeds under cold stress, nine Enshi black pigs were randomly divided into three groups with three pigs in each: a control group (18 ± 2 °C for 58 d), a cold-stress-acclimated group (3 to 8 °C to −17 to −21 °C for 58 d), and an acute cold stress group (−17 to −21 °C for 3 d). RNA-seq technology was used to analyze mRNA and lncRNA expression patterns in subcutaneous adipose tissue under cold stress. The results showed that, under acute cold stress, many metabolic pathways were activated, including those involved in rapid energy supply (e.g., the citric acid cycle/TCA cycle, fatty acid degradation and metabolism, and glycolysis/gluconeogenesis), signal transduction pathways (e.g., PI3K Akt, MAPK, PPAR, HIF-1, mTOR, and FoxO), and immune and cellular homeostasis pathways (chemokine signaling pathway, T cell receptor signaling, Toll-like receptor signaling, and apoptosis and autophagy regulation). Under cold stress acclimation, metabolic regulatory pathways (e.g., AMPK, mTOR, FoxO, HIF-1, glycolysis/gluconeogenesis, and fatty acid degradation), immune and inflammatory regulatory pathways (Toll-like receptors, NOD like receptors, and T/B cell receptor signaling pathways), and signal transduction and cell homeostasis pathways (MAPK, PI3K Akt, NF-κB, Notch signaling pathways, apoptosis, and autophagy regulation) were continuously activated to ensure the stability of adipose tissue structure and function. Acute cold stress activated more pathways than cold stress acclimation, but both led to significant changes in energy metabolism. The results identified the molecular regulatory mechanisms of adipose tissue under cold stress, providing a basis for the subsequent breeding of new cold-resistant pig breeds. Full article

The BONZAI/BON (copine) gene family encodes evolutionarily conserved proteins that modulate the balance between plant defense responses and growth. However, comprehensive identification and functional exploration of BON members have remained largely lacking in wheat. In this study, we identified 10 Triticum aestivum BON (TaBON) members, which are unevenly distributed across seven wheat chromosomes. Phylogenetic analysis clustered these TaBON proteins into two distinct groups. Gene structure and conserved motif analyses revealed high evolutionary conservation within the TaBON family. Cis-acting element analysis revealed that the promoter regions of TaBON genes are enriched with elements responsive to hormones, abiotic stress, and biotic defense signals. Expression profiling further demonstrated distinct transcriptional patterns of TaBON genes in response to infections by Puccinia striiformis f. sp. tritici (stripe rust), Blumeria graminis f. sp. tritici (powdery mildew), Fusarium graminearum, and Zymoseptoria tritici. Overall, this study presents a comprehensive analysis of the TaBON members and provides valuable molecular information for understanding its role in disease resistance. Full article

Cervical cancer (CC) is an alarming global health problem, with predominantly higher incidence, lethal progression, and mortality among women of African ancestry (AA) than women of European ancestry (EA). Although persistent high-risk human papillomavirus (HPV) integration and infection are the key etiological factors, currently available evidence implicates epigenetic reprogramming as a prime contributor to ancestry-associated differences in CC pathogenesis. To address these disparities, we performed genome-wide DNA methylation profiling of HPV-positive cervical intraepithelial neoplasia (CIN) lesions from AA (n = 15) and EA (n = 15) women. Differential methylation analysis identified a distinct epigenomic landscape in AA-CIN lesions, with widespread hypermethylation and hypomethylation at promoter-associated and regulatory CpG sites. Pathway enrichment analyses highlighted dysregulation of ECM-receptor interaction, focal adhesion, PI3K-Akt, MAPK, Ras, Rap1, and RUNX-dependent transcriptional networks. Comparative analysis across CIN grades (CIN1–CIN3) revealed progressive epigenetic reprogramming affecting cell cycles, cytoskeletal dynamics, signaling, and metabolic pathways. Among hypermethylated tumor suppressor genes, SH3GL2 and ARHGAP25 showed significantly higher methylation in AA lesions, accompanied by concomitant loss of their protein expression. MBD1, a methylation-binding regulator, was upregulated in AA-CIN lesions, coinciding with global loss of 5-hydroxymethylcytosine (5hmC), suggesting enhanced transcriptional repression. In contrast, EA lesions retained protein expression and 5hmC levels. Collectively, these findings indicate that early, ancestry-specific epigenetic modifications target tumor suppressor pathways and converge on oncogenic signaling, cytoskeletal remodeling, and cell–cell adhesion. Our study provides mechanistic insight into CC health disparities, identifying SH3GL2 and ARHGAP25 hypermethylation as potential biomarkers, and highlighting epigenetic regulation as a contributor to disparate CC progression in AA women. Full article

Background: Recent advances in spatial transcriptomic technologies enable in situ gene expression profiling while preserving spatial context. This capability is particularly important for studying the tumor microenvironment (TME), where diverse and admixed cell populations interact within highly organized spatial niches that influence tumor progression and therapeutic response. However, the limited resolution of early spatial transcriptomic platforms results in each spatial spot capturing transcripts from multiple cell types, making accurate spot deconvolution or annotation a critical yet challenging step in downstream data analysis. The level of complexity will be particularly prominent in heterogeneous samples like the tumor microenvironments where multiple cell types are highly admixed and reliable single-cell reference atlases may usually be unavailable. Methods: In this paper, we developed our method called STEA, which is a novel and accurate reference-independent enrichment-based annotation algorithm for major cell type. Unlike the existing approaches, STEA does not require single-cell RNA sequencing datasets as reference, offering both flexibility and computational efficiency in execution. Results: We performed comprehensive benchmarking using a variety of simulated datasets across different platforms and scenarios and demonstrated the superior accuracy of STEA. Apart from synthetic data, we also evaluated multiple real datasets to further exemplify its practical applicability on both oncology-related and oncology-unrelated data. More importantly, we could confidently demonstrate the high concordance between prediction of STEA and histological classification by experienced pathologist. Conclusion: Our STEA algorithm provides a practical reference-independent framework to complement the cutting-edge spatial transcriptomics in genomics studies, facilitating accurate downstream high-dimensional spatial characterization of cellular and molecular landscapes, reconstruction of tissue architecture as well as cell–cell communication in malignant and non-malignant scenarios. Taken together, our comprehensive evaluation demonstrates the robustness and reliability of STEA, highlighting its potential as a valuable tool for studying complex tissue organization, particularly within heterogeneous TME. Full article

Background/Objectives: Cellular senescence is a stable growth-arrested state accompanied by the senescence-associated secretory phenotype (SASP), a complex inflammatory secretome that contributes to tissue remodeling, chronic inflammation, and age-related disease. Although multiple signaling pathways have been implicated in SASP regulation, the extent to which interleukin-1 (IL-1) signaling is associated with the organization of SASP-associated transcriptional programs remains incompletely defined at the transcriptomic level. Methods: Here, we performed a focused in silico analysis of a publicly available RNA-sequencing dataset (GSE63577) profiling primary human fibroblasts undergoing replicative senescence. Differential expression analysis revealed broad inflammatory remodeling in senescent fibroblasts, including robust upregulation of canonical SASP-associated cytokines, chemokines, and matrix-related factors. Targeted visualization using a curated, literature-defined SASP gene panel confirmed consistent transcriptional activation of key SASP components during replicative senescence. Results: To assess transcriptional associations, we performed correlation-based network analysis centered on IL1A and IL1B. This analysis demonstrated strong transcriptional coupling between IL-1 signaling components, NF-κB-related genes, and SASP-associated transcripts, revealing a highly connected inflammatory module embedded within the senescence transcriptome. Pathway-level integration using curated gene sets further highlighted IL-1 signaling, cytokine signaling, and NF-κB-related pathways as dominant features of senescence-associated transcriptional changes. These patterns were further supported by analysis of an independent fibroblast senescence dataset (GSE41714), demonstrating consistent IL-1-associated and SASP-related transcriptional trends across experimental systems. Conclusions: Together, these findings suggest that IL-1 signaling is consistently associated with a central position within the SASP-associated transcriptional network during replicative senescence in human fibroblasts. Therefore, the present study contributes transcriptomic network-level evidence supporting an association between IL-1 signaling and coordinated SASP-associated inflammatory programs, and highlights its potential relevance for intervention strategies. Full article

2,4-Dichlorophenoxyacetic acid (2,4-D) is a vital exogenous auxin for the induction and proliferation of litchi embryogenic callus. At present, its molecular regulation mechanism remains unclear. In this study, transcriptome sequencing samples were selected based on different cell growth phenotypes observed in ‘Feizixiao’ litchi embryogenic callus cultured in liquid medium with or without 2,4-D. By integrating transcriptome profiling with weighted gene co-expression network analysis (WGCNA), we identified key genes and signaling pathways dynamically responsive to 2,4-D concentration changes. We identified 558 commonly differentially expressed genes (DEGs), of which 117 were up-regulated and 387 were down-regulated; functional enrichment analysis revealed significant enrichment in the “plant hormone signal transduction” and “phenylpropanoid biosynthesis” pathways. In the former pathway, genes such as AUX28, GH3.17, GH3.6, and ARR5 were up-regulated; in the latter, by comparison, β-glucosidase 47 and Peroxidase 61 exhibited increased expression levels induced by 2,4-D. Furthermore, among these DEGs, 57 transcription factors belonged to 24 families. Notably, VRN1, FEZ, and DOF5.4 were significantly and rapidly induced by 2,4-D. WGCNA results demonstrated a significant positive correlation between the yellow module and 2,4-D treatment. Small heat shock protein (sHSP) genes constituted the core hub genes in the yellow module. Through Venn analysis of DEGs and key modules, 38 cross-genes were identified, of which non-specific lipid-transfer protein-like genes (nsLTP) were found to be specifically up-regulated without 2,4-D. The transcription factors and genes identified work in synergy to ensure the formation and sustained proliferation of embryogenic callus by precisely regulating the dynamic balance of auxin and cytokinin within cells and maintaining the stability of cell structure. Our findings provide a crucial theoretical foundation for understanding the molecular mechanism of 2,4-D in regulating litchi embryogenic callus proliferation. Full article

Chronic obstructive pulmonary disease (COPD) and pulmonary tuberculosis (TB) are major causes of morbidity and mortality worldwide. Epidemiologic studies indicate an increased risk of tuberculosis in patients with COPD; however, the shared molecular mechanisms underlying the pathogenesis of these two diseases remain insufficiently understood. Objective. Based on a comparative bioinformatics analysis of peripheral blood transcriptomic profiles in patients with COPD and pulmonary tuberculosis, to identify common systemic immune mechanisms associated with the pathogenesis of both diseases. Gene expression data from the NCBI GEO public database were analyzed. GSE34608 included blood samples from 8 patients with tuberculosis and 18 healthy controls. The GSE76705 dataset contained peripheral-blood samples from 364 former smokers (225 with COPD and 139 without). Functional enrichment (GO Biological Process and KEGG) was run in ShinyGO; protein–protein interaction networks were built in STRING, and the top-15 hub genes were ranked by the MCC algorithm in CytoHubba. In tuberculosis, 892 up-regulated and 1448 down-regulated genes were identified; in COPD, 520 up-regulated and 1329 down-regulated. Common upregulated DEGs are involved in toll-like receptor signaling pathways, NOD-like receptor signaling pathways, neutrophil extracellular trap (NET) formation, phagosomes, and tuberculosis. Downregulated genes in each of the diseases were associated with processes of transcriptional regulation and RNA metabolism, which may indicate common transcriptional abnormalities in COPD and tuberculosis. COPD and tuberculosis share common pathogenic mechanisms, including the activation of innate immune signaling pathways (TLR, NOD), neutrophilic inflammation, the formation of neutrophil extracellular traps (NETosis), and phagocyte dysfunction. The identified common genes and signaling pathways may serve as a basis for the development of biomarkers and therapeutic targets; however, they require further validation in independent cohorts. Full article