Front Immunol. 2026 Mar 16;17:1822612. doi: 10.3389/fimmu.2026.1822612. eCollection 2026.

ABSTRACT

[This corrects the article DOI: 10.3389/fimmu.2026.1782545.].

PMID:41918731 | PMC:PMC13033988 | DOI:10.3389/fimmu.2026.1822612

Front Pediatr. 2026 Mar 16;14:1770578. doi: 10.3389/fped.2026.1770578. eCollection 2026.

ABSTRACT

The neonatal lung, once considered sterile, is now recognized to harbor a dynamic and complex microbiome that plays a critical role in respiratory health and disease. This review synthesizes current evidence on the composition, development, and functional impact of the lung microbiome in neonates, with a focus on its involvement in key respiratory disorders such as bronchopulmonary dysplasia, respiratory syncytial virus infection, neonatal acute respiratory distress syndrome, cystic fibrosis, and asthma predisposition. We place particular emphasis on the bidirectional communication along the gut-lung axis as a central mechanism, wherein intestinal microbiota and their metabolites modulate pulmonary immunity and inflammation. Emerging multi-omics studies that integrate microbial data with host metabolomic and immune profiles are highlighted for their role in deciphering disease-specific dysbiotic signatures and mechanistic pathways. Critically, this review advances the discussion beyond association by evaluating the translational potential of the microbiome as both a diagnostic biomarker and a therapeutic target. We provide a critical appraisal of innovative microbiome-targeted strategies-including probiotics, postbiotics, phage therapy, and bacterial lysates-and discuss the unique challenges and future directions for translating these approaches into safe, effective clinical interventions for vulnerable neonates. By bridging foundational science with clinical implications, this work aims to inform the development of novel, ecology-informed therapeutics to prevent and mitigate neonatal respiratory diseases.

PMID:41918694 | PMC:PMC13033698 | DOI:10.3389/fped.2026.1770578

Cancer Immunol Immunother. 2026 Mar 31;75(4):126. doi: 10.1007/s00262-026-04368-1.

ABSTRACT

While anti-programmed death-1 (anti-PD-1) therapy has revolutionized lung cancer treatment, its efficacy remains limited by an immunosuppressive tumor microenvironment (TME). We therefore investigated whether combining anti-PD-1 inhibitor with catgut embedding at the Zusanli acupoint (CIAA) could enhance anti-tumor immunity by reprogramming the TME in a lung cancer mouse model. Combining in vivo tumor monitoring, multi-parametric immune profiling (flow cytometry, IHC, ELISA), and multi-omics analyses (transcriptomics and metabolomics), we found that the combination therapy was associated with enhanced tumor growth inhibition. This effect correlated with a comprehensive TME transformation: conversion to an immunologically active state with increased effector immune cell infiltration (CD8⁺ T, CD4⁺ T, B cells, macrophages) and decreased regulatory T cells, coupled with suppression of pro-tumorigenic factors (VEGF, IL-6). Integrated omics analysis suggests that the combined treatment may modulate tumor-stroma interaction pathways (e.g., PI3K-Akt, focal adhesion) and rewire immunometabolic networks (e.g., tryptophan metabolism). Our study provides hypothesis-generating correlative data positioning CIAA as a potential adjunct capable of remodeling the TME to potentiate anti-PD-1 therapy in lung cancer.

PMID:41915222 | PMC:PMC13038699 | DOI:10.1007/s00262-026-04368-1

Zhonghua Yi Xue Za Zhi. 2026 Mar 31;106:1-7. doi: 10.3760/cma.j.cn112137-20251201-03143. Online ahead of print.

ABSTRACT

Objective: To analyze the association between molecular typing and prognosis with recurrence pattern in triple-negative breast cancer (TNBC) patients based on long-term follow-up of a multi-omics cohort. Methods: A retrospective analysis was performed on the clinical data and transcriptomic data of patients diagnosed with TNBC at Department of Breast Surgery, Fudan University Shanghai Cancer Center from January 1, 2007, to December 31, 2014. The survival status of patients was documented, and the follow-up continued until the patients' death or August 31, 2025. According to the"Fudan subtype", the patients were categorized into the basal-like immune suppressed (BLIS), immunomodulatory (IM), luminal androgen receptor (LAR), and mesenchymal-like (MES). Survival curves were plotted using the Kaplan-Meier method, and the log-rank test was employed to evaluate the differences in overall survival (OS), disease-free survival (DFS) and recurrence-free interval (RFI) among TNBC patients with different molecular subtypes. Multivariate Cox proportional hazards regression analysis was used to assess the association between"Fudan subtype"and OS, DFS and RFI. Differential expression analysis and subsequent gene set enrichment were conducted. Competing-risk models were used to calculate the cumulative incidence of lung metastasis after accounting for competing events, and the differences were assessed using the Fine-Gray test. Results: After excluding 9 patients lost to follow-up, a total of 351 patients with TNBC were included in the analysis. The mean age at baseline was 53.46±11.36 years, and the median follow-up duration was 102.09 months. During follow-up, 72 patients died and 84 experienced recurrence or metastasis. Among them, 134 patients were classified as the BLIS subtype, with 27 deaths (20.15%); 86 patients were classified as the IM subtype, with 11 deaths (12.79%); 81 patients were classified as the LAR subtype, with 22 deaths (27.16%); and 50 patients were classified as the MES subtype, with 12 deaths (24.00%). The 10-year RFI rates for the BLIS, IM, LAR, and MES subtypes were 80.12% (95%CI: 73.41%-87.44%), 92.35% (95%CI: 86.64%-98.43%), 81.92% (95%CI: 73.39%-91.44%), and 72.95% (95%CI: 61.37%-86.71%), respectively. Kaplan-Meier survival curves showed that the differences of RFI among the four molecular subtypes of patients were statistically significant (P=0.040). Multivariate analysis showed that LAR subtype (LAR vs IM, HR=2.41, P=0.042) was the independent risk factor for DFS, and BLIS subtype (BLIS vs IM, HR=4.17, P=0.011), LAR subtype (LAR vs IM, HR=3.49, P=0.040) and MES subtype (MES vs IM, HR=3.98, P=0.019) were independent risk factors for RFI. The BLIS subtype is more likely to develop recurrence or metastasis in the early postoperative period, particularly lung metastasis. Differential gene expression analysis showed that BLIS subtype-specific genes, including those involved in proliferation and cell cycle activity, were predominantly upregulated in tumors with early recurrence or metastasis. Competing-risk analysis demonstrated that BLIS patients had a higher cumulative incidence of lung metastasis both overall and within the first 5 years after surgery compared with non-BLIS patients (both P<0.05). Conclusion: The"Fudan subtype"was significantly associated with RFI in early-stage TNBC patients. In addition, recurrence and metastasis were more likely to be observed in the early postoperative period in the BLIS subtype, particularly early lung metastasis.

PMID:41913624 | DOI:10.3760/cma.j.cn112137-20251201-03143

EMBO Mol Med. 2026 Mar 30. doi: 10.1038/s44321-026-00410-y. Online ahead of print.

ABSTRACT

Lung cancer is the leading cause of cancer-related mortality worldwide, with lung squamous cell carcinoma (LUSC) comprising 20-30% of cases. Immunochemotherapy (IC) is the standard first-line treatment for advanced LUSC, yet reliable predictors of therapeutic response remain unavailable. Using single-cell multi-omics profiling of paired pre- and post-treatment tumor and blood samples, we observed that patients responding to IC exhibited significantly higher baseline levels of peripheral blood monocytes, tumor-infiltrating classical monocytes, and APOBEC3A+ monocytes across both compartments compared with non-responders. These associations were independently validated in additional cohorts using routine complete blood count testing and multiplex immunofluorescence analysis of native tumor tissues. Our findings reveal monocyte-related parameters as clinically accessible indicators that link systemic immunity with the tumor microenvironment and hold promise for predicting IC responsiveness in patients with LUSC.

PMID:41912871 | DOI:10.1038/s44321-026-00410-y

Cancer Lett. 2026 Mar 28;648:218465. doi: 10.1016/j.canlet.2026.218465. Online ahead of print.

ABSTRACT

Cancer remains a leading cause of death worldwide, with lineage plasticity emerging as a hallmark that drives therapy resistance and tumor progression by enabling cancer cells to alter identity and evade targeted therapies. Although genomic and transcriptomic aberrations correlate with lineage plasticity, the absence of scalable cross-cancer markers to rapidly identify plastic subtypes has limited predictive utility. Homeobox (HOX) genes encode transcription factors that define tissue identity through distinct expression patterns, or HOX codes, within specific lineages. By analyzing multi-omics data encompassing 39 HOX genes across more than 80,000 RNA-seq samples across 23 cancer types spanning 114 cancer subtypes, we found that HOX code expression robustly stratifies lineage-constrained and lineage-plastic states at a cross-cancer level. This framework revealed previously unrecognized lineage-plastic subtypes in prostate cancer, lung cancer, and acute myeloid leukemia (AML), each displaying distinct HOX code divergence compared to non-plastic counterparts. Differential expression analysis across these representative malignancies identified RUNX1T1 as a consistent regulator associated with HOX-defined plastic states. We validated RUNX1T1 upregulation in bulk and single-cell RNA-seq from extensive preclinical and clinical cohorts and demonstrated that RUNX1T1 is functionally required for lineage-plastic programs in prostate cancer models. AI-based structural modeling and co-immunoprecipitation established the NCOR/HDAC3 complex as a critical binding partner of RUNX1T1. CUT&RUN profiling revealed that RUNX1T1 remodels chromatin by globally reducing active enhancer marks, thereby repressing lineage-defining differentiation programs and reshaping HOX positional identity. Selective pharmacologic inhibition of HDAC3 or targeted gene silencing via lipid nanoparticles suppressed the growth of lineage-plastic cancer cells, uncovering a therapeutically actionable vulnerability. Together, these findings establish RUNX1T1 as a cross-lineage regulator of HOX code-defined plasticity and identify the RUNX1T1-HDAC axis as a targetable mechanism underlying cancer lineage plasticity.

PMID:41912135 | DOI:10.1016/j.canlet.2026.218465

Microb Pathog. 2026 Mar 28;215:108464. doi: 10.1016/j.micpath.2026.108464. Online ahead of print.

ABSTRACT

Despite the clinical application of Ophiopogon japonicus in idiopathic pulmonary fibrosis (PF), its key anti-fibrotic components and underlying mechanisms remain poorly defined. Using a bleomycin-induced murine PF model, we systematically compared the efficacy of the total extract (OJTE), polysaccharides (OJTP), saponins (OJTS), and flavonoids (OJTF). The active component was further investigated via integrated metagenomics and metabolomics (serum/feces) to decipher the gut-lung axis mechanism. All O. japonicus components attenuated lung injury and collagen deposition, with OJTP demonstrating the most potent efficacy (reducing lung hydroxyproline content by 42.12% (p < 0.01) compared to the model group). Multi-omics analysis revealed that OJTP remodeled the gut microbiota, notably enriching probiotic strains such as Muribaculaceae bacterium (log₂FC = 2.17) and Duncaniella muricolitica (log₂FC = 2.06), as well as the polysaccharide-utilizing species Prevotella sp. MGM2 (log₂FC = 2.79). Concomitantly, OJTP significantly altered host metabolism, upregulating key metabolites including urobilinogen (p < 0.0001) and 5-amino valeric acid betaine (5-AVAB, p < 0.002). These metabolites are implicated in porphyrin and amino acid metabolism, respectively. Correlation networks further established strong associations between these OJTP-modulated microbes and metabolites. Our study first identifies OJTP as the primary bioactive component of O. japonicus against PF. We propose a novel trans-organ mechanism wherein OJTP ameliorates PF via orchestrating a "gut microbiota-metabolite" axis, highlighting the therapeutic potential of targeting polysaccharide-probiotic synergy.

PMID:41912071 | DOI:10.1016/j.micpath.2026.108464

J Vis Exp. 2026 Mar 13;(229). doi: 10.3791/70383.

ABSTRACT

This study utilized a multi-omics and computational biology framework to investigate the therapeutic potential of the Traditional Chinese Medicine (TCM) formula Buti Huatan Tang (BTHTT) against chronic obstructive pulmonary disease (COPD). Significant physiological improvements were observed in a rat model following BTHTT intervention. Histological analysis showed a reversal of lung pathological damage, while biochemical assays, and transcriptomics confirmed the normalization of IL-1β and IL-1R2 levels. Additionally, metabolic profiling revealed that BTHTT corrected disruptions in T3 and T4 thyroid hormone levels. A negative correlation was observed between the IL-1β/IL-1R2 axis and these thyroid hormones, indicating that their regulation is associated with the formula's therapeutic effect. Beyond direct measurements, machine learning algorithms identified ten COPD signature genes from clinical databases. Pathway enrichment analysis suggests that BTHTT may act through cytokine-cytokine-receptor interactions and thyroid hormone synthesis pathways. Furthermore, while 283 components were identified in vivo, compounds such as tanshinone IIA and cryptotanshinone are currently considered candidate active substances. Their role as primary drivers is supported by a model in which they stably bind to IL-1R2; this inference is based on molecular docking and molecular dynamics (MD) simulations rather than direct experimental isolation. Overall, the data support a model in which BTHTT exerts a multi-target effect on COPD by modulating inflammation and metabolic homeostasis. This integrated approach provides a refined scientific basis for the clinical application of BTHTT and highlights specific pathways for future experimental validation.

PMID:41911070 | DOI:10.3791/70383

Front Immunol. 2026 Mar 13;17:1770348. doi: 10.3389/fimmu.2026.1770348. eCollection 2026.

ABSTRACT

Interstitial lung disease (ILD) is one of the most common extra-articular manifestations of rheumatoid arthritis (RA). Some patients with RA-ILD may develop progressive pulmonary fibrosis, leading to severe impairment of lung function and respiratory failure, which impacts quality of life and can even be life-threatening. This review identified genetic susceptibility, environmental factors, and immune dysregulation as key contributors to the etiology and pathogenesis of RA-ILD. We highlight that autoantibodies, adaptive immune abnormalities, and tertiary lymphoid organ formation significantly drive pulmonary inflammation and fibrosis, while pro-inflammatory cytokines and epithelial-mesenchymal transition (EMT) further contribute to lung tissue injury. Current treatment options, including glucocorticoids, immunosuppressants, and antifibrotic agents such as nintedanib and pirfenidone, are often limited by substantial side effects. Additionally, emerging therapies like JAK inhibitors, CAR-T cells, and the upcoming phosphodiesterase-4B inhibitor, nerandomilast, show promise, but no curative treatment exists to date. Future research could focus on multi-omics technologies and conducting multicenter clinical trials to establish therapeutic targets and advance precision medicine for RA-ILD.

PMID:41909710 | PMC:PMC13021622 | DOI:10.3389/fimmu.2026.1770348

J Ethnopharmacol. 2026 Mar 26;365:121591. doi: 10.1016/j.jep.2026.121591. Online ahead of print.

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Acute lung injury (ALI) lacks effective therapies. HIF-1α-driven glycolysis can promote histone lactylation and sustain pro-inflammatory (M1) macrophage responses. Daxiefei Decoction (DXFD), a classic traditional Chinese medicine formula, is used for pulmonary inflammatory diseases, but its immunometabolic mechanism remains unclear.

AIM OF THE STUDY: To evaluate the protective efficacy of DXFD against lipopolysaccharide (LPS)-induced ALI and to determine whether it acts through the HIF-1α/glycolysis/histone H3K18 lactylation (H3K18la) axis to regulate macrophage polarization.

MATERIALS & METHODS: DXFD constituents were characterized by UPLC-LTQ-Orbitrap-MS/MS, followed by network pharmacology, molecular docking, and molecular dynamics (MD) simulations. Lung transcriptomics and metabolomics were performed in ALI mice. Efficacy and mechanisms were assessed in LPS-challenged mice and RAW264.7 macrophages using histopathology, ELISA, qRT-PCR, Western blotting, and immunofluorescence. HIF-1α overexpression was used for validation.

RESULTS: DXFD dose-dependently alleviated lung injury and reduced pro-inflammatory cytokines in vivo, and suppressed M1 polarization in vivo and in LPS-stimulated macrophages. Multi-omics indicated activation of HIF-1α-associated inflammatory and glycolytic programs in ALI, which were normalized by DXFD. DXFD decreased glycolytic enzyme expression and reduced histone H3K18 lactylation (H3K18la); these effects were partially reversed by HIF-1α overexpression. Molecular docking and dynamics suggested stable binding of baicalin to HIF-1α.

CONCLUSIONS: DXFD mitigates ALI by dampening HIF-1α-dependent glycolysis and H3K18la, thereby restraining M1-driven inflammatory amplification.

PMID:41903585 | DOI:10.1016/j.jep.2026.121591

Pathogens. 2026 Feb 27;15(3):254. doi: 10.3390/pathogens15030254.

ABSTRACT

Pulmonary tuberculosis (TB) remains a major global health challenge. The molecular and metabolic responses of monocyte-derived macrophages (MDMs), which are critical for host defense against Mycobacterium tuberculosis (Mtb), are not fully characterized. A murine pulmonary TB model was established by intravenous injection of BALB/c mice with the attenuated Mtb strain H37Ra; controls received saline. After 8 weeks, lung MDMs were isolated for integrated transcriptomic and untargeted metabolomic profiling. Transcriptomic analysis identified 3970 differentially expressed genes (DEGs) in infected MDMs, including upregulated Ptpn1, Dgat2, and Alox5ap and downregulated Cyld, Zfp61, and Mapk11. Metabolomic profiling revealed 113 differentially accumulated metabolites (DAMs). Taurocholic acid and linoleic acid were identified as potential diagnostic biomarkers, both achieving an area under the curve (AUC) of 1.0 in ROC analysis. Integrated omics analysis showed a positive correlation between linoleic acid levels and the expression of Tbxas1, Acaa1b, and Acox1, implicating lipid metabolic pathways in the host response to TB. This multi-omics study delineates key molecular and metabolic alterations in lung MDMs during TB infection. The identified metabolites, taurocholic acid and linoleic acid, show promise as biomarkers, while dysregulated linoleic acid metabolism represents a potential target for novel diagnostic and therapeutic strategies against TB.

PMID:41901707 | PMC:PMC13029415 | DOI:10.3390/pathogens15030254

Curr Issues Mol Biol. 2026 Feb 26;48(3):247. doi: 10.3390/cimb48030247.

ABSTRACT

Lung cancer remains a leading cause of cancer mortality worldwide and continues to impose substantial clinical and economic burdens. Beyond tumor-intrinsic oncogenic drivers, disease progression and therapy response are shaped by the tumor microenvironment (TME), including immune cells, cancer-associated fibroblasts (CAFs), endothelial cells, extracellular matrix, inflammatory mediators, etc. In lung cancer, chronic injury from tobacco smoke, airway disease, and treatment itself remodels local tissue programs that can either support antitumor immunity or promote immune exclusion, fibrosis, and metastatic seeding. Here, we analyze recent evidence linking lung tumorigenesis to TME ecology across histologies, with emphasis on CAF heterogeneity, spatial organization of immune niches, and the distinct microenvironments that govern organ-specific metastasis (including brain metastasis). We also evaluate emerging therapeutic strategies that aim to target or reprogram the TME, including perioperative immune checkpoint blockade, combined immunotherapy-radiotherapy approaches, and pathways such as IL-6 and TGF-β that coordinate immune suppression and stromal remodeling. Finally, we outline key gaps and potential future directions, such as longitudinal and spatial multi-omics, better biomarkers of stromal state, and trial designs that account for dynamic microenvironmental adaptation.

PMID:41899399 | PMC:PMC13025777 | DOI:10.3390/cimb48030247

Int J Mol Sci. 2026 Mar 23;27(6):2884. doi: 10.3390/ijms27062884.

ABSTRACT

Ducks, once considered mere reservoirs, now serve as both victims and amplifiers of persistent highly pathogenic avian influenza (HPAI) virus cycles in wild populations. The molecular pathogenesis of HPAI is shaped by complex, dysregulated molecular networks, necessitating a systems biology approach that integrates computational modeling of host-pathogen interactions. Despite recent advances, a comprehensive understanding of the signaling pathways, molecular mechanisms, and hub genes driving HPAI H5N1 pathogenesis in avian hosts remains incomplete. This study addresses this gap by employing an integrated multi-omics strategy-combining transcriptomic, proteomic, and phosphoproteomic analyses-to map the signaling networks and key host factors involved in HPAI H5N1 infection in duck lung tissue. Our network analysis revealed activation of RIG-I-like receptor, toll-like receptor, NOD-like receptor, NF-κB, and JAK/STAT signaling pathways. Phosphoproteomic profiling independently confirmed the activation of these pathways, supporting the integrated network findings. Key regulatory hub genes identified include STAT1, DDX58 (RIG-I), MYD88, NFKBIA, NFKB1, IRF7, SOCS3, ACTB, TLR4, TLR7, IL-6, CASP1, and CASP8, which form a central hub in duck antiviral immunity. Some of these genes may represent promising targets for therapeutic or vaccine development against avian influenza. Collectively, this work delineates the critical signaling pathways and hub genes underlying HPAI H5N1 pathogenesis in ducks through comprehensive multi-omics integration.

PMID:41898742 | PMC:PMC13026356 | DOI:10.3390/ijms27062884

Cells. 2026 Mar 22;15(6):566. doi: 10.3390/cells15060566.

ABSTRACT

Chronic exposure to benzo[a]pyrene (BaP), a Group 1 IARC carcinogen, is a major driver of lung carcinogenesis; however, how sustained subcytotoxic exposure reprograms bronchial epithelium toward preneoplastic states remains poorly defined. Here, we subjected BEAS-2B human bronchial epithelial cells to 12 weeks of continuous BaP at environmentally relevant concentrations (0.1 and 1.0 µM) and interrogated the resulting phenotypes using an integrated multi-scale framework encompassing functional toxicology, RT-qPCR, RNA-seq, phospho-kinase/NF-κB arrays, and organotypic air-liquid interface (ALI) cultures. Cells maintained metabolic competence throughout, evidenced by sustained CYP1A1 and CYP1B1 induction at both acute (4 h) and chronic (12-week) timepoints, while accumulating genotoxic stress as demonstrated by dose-dependent nuclear γ-H2AX foci formation and ATM phosphorylation (Ser1981). RNA-seq revealed a dose-dependent transcriptional shift: 0.1 µM BaP yielded 119 differentially expressed genes (DEGs; |log2FC| ≥ 1, FDR < 0.05), whereas 1.0 µM generated 255 DEGs. Downregulated transcripts were enriched for extracellular matrix and cell-adhesion programs (COL14A1, ADAMTS2, CSMD3, CADM3), while upregulated genes encompassed inflammatory, calcium-signaling, and vesicle-trafficking modules (NFATC4, CSF2RA, SYT1, PCLO). Phospho-kinase/NF-κB arrays confirmed a p53/NF-κB signaling nexus, with concurrent activation of MAPK/ERK (Thr202/Tyr204) and PI3K/Akt (Ser473) pathways. Despite persistent genotoxic stress, cells did not acquire anchorage-independent growth and remained non-tumorigenic in vivo. Critically, ALI organotypic cultures derived from BaP-exposed cells exhibited histological dysplasia, nuclear pleomorphism, and disrupted apical-basal polarity. These findings mechanistically link chronic BaP exposure to an initiation-like preneoplastic state and establish a validated 2D/3D multi-omics platform for PAH-driven lung carcinogenesis research.

PMID:41892355 | PMC:PMC13025689 | DOI:10.3390/cells15060566

Biology (Basel). 2026 Mar 12;15(6):461. doi: 10.3390/biology15060461.

ABSTRACT

This study investigates the mechanisms underlying drought adaptability in Duolang sheep, a local breed from two distinct habitats in Xinjiang-an arid southern region and a grassland northern region-aiming to identify key factors driving differential environmental adaptation. Integrated multi-omics analyses were performed, including serum biochemical assays, untargeted metabolomics of perirenal and tail fat tissues, and transcriptomic profiling of lung, liver, and kidney samples. Our results revealed notable differences: (1) serum levels of GSH-Px, IL-2, and IgG were significantly higher in the southern group (p < 0.01); (2) metabolomic analysis identified key differential metabolites, including EPA (involved in unsaturated fatty acid biosynthesis), choline (glycerophospholipid metabolism), L-serine and glutathione (cofactor biosynthesis), and taurine (sulfur metabolism); and (3) transcriptomic analysis revealed significant differential expression of genes such as FGF21 (thermogenesis), CD14 and DUSP2 (MAPK signaling pathway), GOT1 (arginine biosynthesis), and AVPR2 (vasopressin-regulated water reabsorption). Integrative correlation analysis further indicated that glutathione, EPA, GOT1, and CD14 are involved in energy and lipid metabolism, while taurine, AVPR2, and DUSP2 contribute to oxidative stress resistance and immune regulation. These molecular and metabolic adjustments collectively enhance drought adaptability in southern Xinjiang Duolang sheep. In conclusion, adaptation to arid environments requires enhanced antioxidant capacity and immune function, with metabolites such as EPA supporting lipid metabolism and genes such as FGF21 regulating fatty acid oxidation to limit triglyceride accumulation.

PMID:41892221 | PMC:PMC13023672 | DOI:10.3390/biology15060461

J Asthma Allergy. 2026 Mar 19;19:575312. doi: 10.2147/JAA.S575312. eCollection 2026.

ABSTRACT

Systems biology approaches have contributed to advancing our understanding of complex respiratory diseases including asthma and chronic obstructive pulmonary disease (COPD). This systematic review evaluates the application of systems biology methodologies in respiratory medicine, focusing on multi-omics data integration and computational techniques for biomarker discovery and mechanistic understanding. Following PRISMA 2020 guidelines, we conducted a comprehensive literature search across Web of Science and Scopus databases, identifying 117 peer-reviewed documents published from 2010 to 2024. The review methodology employed bibliometric analysis combined with qualitative synthesis of included studies. Results demonstrate steady growth in systems biology applications for asthma and COPD research, with publication rates increasing by approximately 0.5 articles per year (R² = 0.73, p < 0.001). Bibliometric analysis identified five major research clusters: systems biology as a foundational methodological framework (Basic Theme), COPD-focused research as the most developed area (Motor Theme), gene expression analysis, disease classification approaches, and specialized lung disease investigations (Niche Theme). Multi-omics integration studies achieved 82-91% accuracy in disease classification tasks, with transcriptomics-based asthma endotyping validated in over 1500 patients across multiple cohorts. Network analysis approaches identified hub genes (IL-6, TNF-α, MMP9) replicated across three independent studies. Machine learning applications demonstrated 80-90% accuracy for diagnostic and prognostic tasks, though external validation remains limited, with only 15% of reviewed studies including independent validation cohorts. Significant challenges persist in data integration, computational reproducibility, and clinical translation. Most studies employed modest sample sizes (median n=89), and population diversity was limited, with 89% conducted in European-ancestry populations. This review provides a comprehensive assessment of systems biology progress in respiratory medicine, identifies methodological gaps, and highlights the need for standardized protocols, larger collaborative studies, and rigorous external validation to advance clinical implementation of systems biology findings in asthma and COPD management.

PMID:41878747 | PMC:PMC13007689 | DOI:10.2147/JAA.S575312

Immunotherapy. 2026 Mar 24:1-13. doi: 10.1080/1750743X.2026.2648431. Online ahead of print.

ABSTRACT

The gut microbiota (GM) has emerged as a key modulator of cancer development and therapeutic response beyond the gastrointestinal tract. In extra-intestinal cancers, GM composition influences oncogenesis, with specific microbial taxa and their metabolites linked to either increased or decreased cancer risk, as highlighted by Mendelian Randomization studies. Beyond cancer initiation, GM plays a critical role in shaping the efficacy and toxicity of anticancer therapies, particularly immunotherapy. We searched PubMed and ClinicalTrials.gov using the terms"gut microbiota," "immune checkpoint inhibitors," "faecal microbiota transplantation," "solid tumor" in oncology patients. Evidence indicates that SCFA-producing bacteria, Akkermansia muciniphila, and members of Lachnospiraceae and Ruminococcaceae families enhance responses to immune checkpoint inhibitors (ICIs), whereas dysbiosis and immunosuppressive bacteria are associated with poor outcomes and immune-related adverse events. Therapeutic modulation of the GM through probiotics, prebiotics, fecal microbiota transplantation, and dietary interventions shows promise in optimizing immunotherapy efficacy, yet standardized clinical protocols remain lacking. Integrating GM profiling with multi-omics and artificial intelligence approaches offers a path toward personalized microbiota-targeted interventions to improve patient outcomes. This review critically summarizes current evidence linking GM to cancer immunotherapy, discusses mechanistic insights, and outlines future perspectives for translating microbiota modulation into clinical practice.

PMID:41873461 | DOI:10.1080/1750743X.2026.2648431

J Ethnopharmacol. 2026 Mar 21:121548. doi: 10.1016/j.jep.2026.121548. Online ahead of print.

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: The Tingli Dazao Xiefei Decoction (TD) is a traditional phlegm-eliminating prescription composed of Descurainia sophia (L.) Webb. ex Prantl (TLZ) and Ziziphus jujuba Mill. (DZ), which can relieve lung, heart and kidney injury in asthma. TLZ acts as the monarch drug in the TD. Based on the research mode of "material basis of traditional Chinese medicinal properties can be divided and combined", we have confirmed that the flavonoid glycosides components /the oligosaccharide components/the fatty oil component (FG/Oli/FO) are effective components of TLZ. However, the compatibility mechanism of the TD, and the contribution of the effective components of TLZ to the efficacy were still unclear.

AIM OF THE STUDY: To clarify the compatibility mechanism of TD, and the contribution of the effective components of TLZ to the efficacy from a comprehensive perspective of lung, heart, and kidney.

METHODS: First, we chose the asthma model corresponding to the efficacy of TD in purging the lungs and relieving asthma, and the rats were divided into the normal (NC) group, model (M) group, dexamethasone (DEX) group, and treatment groups of TD/TLZ/DZ/FO+DZ/Oli+DZ/FG+DZ. Second, metabolomics and network pharmacology were applied to elucidate the comprehensive protective effect of TD/FG+DZ/Oli+DZ/FO+DZ. Third, the multi-omics results were validated using Western blotting, RT-qPCR, flow cytometry, and immunofluorescence.

RESULTS: FO+DZ/Oli+DZ/FG+DZ had different degrees of protective effects against lung/heart/kidney injury in asthma. In metabolomics research, the principal component analysis (PCA) and cluster analysis results showed that the TLZ group was closer to TD group than DZ group, the FO+DZ and Oli+DZ group clustered with TD/NC groups in the lung and kidney, and the FO+DZ and FG+DZ group clustered with TD/NC groups in the heart. Pathway enrichment analysis suggested that the comprehensive protective effect of TLZ and its effective components combined with DZ on lung/heart/kidney may be achieved by regulating the arginine and proline metabolism, alanine, aspartate and glutamate metabolism, and unsaturated fatty acid biosynthesis. Multi-organ metabolomics and network pharmacology revealed consistent biological functions in KEGG pathways. Validation experiment showed that TLZ and its effective components combined with DZ could reverse the abnormal expression of proteins and RNA related to inflammation, airway remodeling, excitotoxicity, and energy-supply, apoptosis at different levels. Furthermore, FO+DZ may reduce asthma damage by inhibiting the FABP4/PPAR-γ/NF-κB signaling pathway.

CONCLUSION: TLZ played the key role in TD, and FO had the best therapeutic effect on each organ; the efficacy of Oli was mainly reflected in reducing lung and kidney damage, and FG was mainly involved in enhancing energy metabolism in the heart. These findings proved that traditional Chinese medicine could exert comprehensive efficacy in a 'multi-components trigger multi-channel' way.

PMID:41871629 | DOI:10.1016/j.jep.2026.121548

Sci China Life Sci. 2026 Mar 16. doi: 10.1007/s11427-025-3273-6. Online ahead of print.

ABSTRACT

Phenotypic diversity of malignant cells within a tumor underlies intratumor heterogeneity (ITH), a key determinant of cancer metastasis and treatment failure. However, the molecular mechanisms driving this heterogeneity are poorly understood. Here, we curated and analyzed a cohort of 3' tag-based single-cell RNA-seq covering 12 common cancer types. We identified thousands of poly(A) site (PAS) peaks representing the 3' ends of previously unannotated transcripts, whose expression is widely associated with diverse malignant cellular states. By integrating multi-omics data, we characterized the expression patterns and epigenetic landscape of these unannotated PAS peak-associated transcripts (UPTs). The expression heterogeneity of UPTs was supported by multi-region sampling bulk RNA-seq data and recapitulated within cancer cell lines. As proof of principle validation, functional experiments confirmed that two noncoding UPTs promoted the proliferation and migration of lung cancer cells. Our results suggest that epigenetic activation of unannotated noncoding transcripts might represent a previously unrecognized mechanism contributing to transcriptomic ITH.

PMID:41870780 | DOI:10.1007/s11427-025-3273-6

Discov Oncol. 2026 Mar 23. doi: 10.1007/s12672-026-04893-6. Online ahead of print.

ABSTRACT

BACKGROUND: Lung cancer remains the leading cause of cancer-related mortality worldwide. This study aimed to develop prognostic prediction models for lung squamous cell carcinoma (LUSC) through multi-omics integration using Mendelian randomization analysis.This study addresses a critical gap in lung cancer research through two complementary approaches in major lung cancer subtypes: (1) hypothesis-generating multi-omics analysis in LUSC to identify prognostic biomarkers and characterize the metabolic-immune landscape. This integrated framework provides both predictive tools for personalized medicine and mechanistic insights into metabolic causality.

METHODS: Multi-omics analysis was performed using TCGA data, including RNA-seq, DNA methylation, and whole-exome sequencing. Machine learning models incorporating 15 algorithms were developed and externally validated in two independent GEO cohorts. Mendelian randomization analysis assessed causal relationships between 32 lipid metabolites and SCLC risk. RT-qPCR experiments validated key prognostic genes in lung squamous cell carcinoma (LUSC) cell lines.

RESULTS: The optimal machine learning model (StepCox [forward] + Random Survival Forest) demonstrated superior performance with C-index of 0.73 in internal testing and 0.71 and 0.68 in external validation cohorts. High CD8 + T cell and M1 macrophage infiltration was associated with favorable prognosis. Most lipid metabolites showed no significant causal associations with SCLC risk after multiple testing correction, though two phosphatidylcholine metabolites demonstrated potential protective effects. RT-qPCR validation confirmed significant upregulation of all four key genes in LUSC cell lines.

CONCLUSIONS: This study successfully developed robust machine learning-based prognostic models for LUSC with clinical utility for risk stratification and provided evidence that lipid alterations in lung cancer are likely downstream consequences rather than causal drivers of tumorigenesis.

PMID:41870745 | DOI:10.1007/s12672-026-04893-6