Gut Microbiota
Dietary whey protein protects against Crohn's disease via the gut phageome and bacteriome
Su R, Wen W, Jin Y, et al. Dietary whey protein protects against Crohn's disease by orchestrating cross-kingdom interaction between the gut phageome and bacteriome. Gut 2025; 74(8): 1246-1260. doi: 10.1136/gutjnl-2024-334516.
Dietary influence on the development and/or propagation of Crohn’s disease remains a key interest. Diet is a potent modulator of the gut microbiome (community of microorganisms in the gut), which in turn impacts intestinal inflammation.
However, less is known about the gut phageome that refers to the viral component of the microbiome, made up of bacteriophages that influence bacterial populations and microbial diversity. In this article, Su et al. explore the impact of diet on the gut phageome by obtaining terminal ileal biopsy samples to assess the mucosal microbiome from 140 patients (70 Crohn’s, 70 healthy controls) alongside dietary data. They initially identified that Whey Protein (WP) significantly impacts the gut phageome. When extrapolating this new information to data from the IBD UK Biobank, they found that consumers (versus non-consumers) showed higher differences in alpha-diversity of the phageome (i.e., more variety and balance), particularly against pathogenic bacteria, without differences to the bacteriome.
Su et al. then conducted a series of in vivo murine experiments to prove that WP is causally associated with reduced intestinal inflammation. First, WP-fed mice were protected from dextran sulphate sodium-induced inflammation (toxic to intestinal epithelium). Second, WP-fed mice had higher upregulation of genes related to immune protection. Third, by looking at the faecal microbiome at different timepoints, WP appeared to temporally reshape both the phageome and bacteriome towards populations that help resist intestinal inflammation. This final point was confirmed by faecal transplantation from the WP-fed mice to unfed recipients that led to an attenuated inflammatory response. These effects appeared to be mediated by recusing the inhibitory effects of A. muciniphila on S. thermophilus through phage-mediated lysis in a series of further experiments to investigate this proposed phage-bacteria-inflammatory cascade. Take collectively, Su et al. provide important evidence into the role of diet and cross-kingdom interaction for the maintenance of gut health.
Gut microbial-derived N-acetylmuramic acid alleviates colorectal cancer via the AKT1 pathway
Hu M, Xu Y, Wang Y, et al. Gut microbial-derived N-acetylmuramic acid alleviates colorectal cancer via the AKT1 pathway. Gut 2025; 74(8): 1230-1245. doi: 10.1136/gutjnl-2024-332891.
Evidence has started emerging that metabolites of the intestinal microbiota influence colorectal cancer (CRC) development. Peptidoglycan fragments (PGFs), as one such group of these, whilst previously shown to contribute to maintenance of intestinal homeostasis, make an as yet unclear contribution to CRC pathogenesis. This work looked to explore the role of PGFs in development of intestinal neoplasia.
This was evaluated through a suite of studies. The relative abundance of genes responsible for peptidoglycan synthases/hydrolases was assessed by metagenomic analysis. Using targeted mass spectrometry, quantification of certain PGFs (stool and serum) of CRC patients was performed. Direct effects of PGFs were examined in organoids derived from CRC patients, as well as mouse models. Finally, a combination of proteome microarray, transcriptome sequencing and rescue assays were used to examine their downstream molecular targets.
In terms of findings, among 1121 CRC cases, a significant reduction in relative abundance of peptidoglycan synthase genes was demonstrated. Mass spectrometry data showed patients with CRC had significantly lower levels of a specific PGF – N-acetylmuramic acid (NAM) – which decreased as tumours progressed. In patient-derived CRC organoids – NAM – was also demonstrated to inhibit growth proportionate to its concentration, and inhibited tumour development in multiple mouse models, in addition. Finally, subsequent studies assessing downstream effects, suggested inhibition by NAM of AKT1 (RAC(Rho family)-alpha serine/threonine-protein kinase) activation (through direct binding thus blocking phosphorylation) to represent a potential mechanism of action.
In conclusion, in addition to their established role in intestinal homeostasis, this group has generated novel evidence of the possible role of PGFs in intestinal tumorigenesis, with an apparent paucity of such molecules (specifically NAM) in the setting of CRC, and a potential inhibitory effect of them in a human organoid/mouse setting, possibly effected via the AKT1 signalling pathway. PGFs (NAM, in particular) may therefore represent an exciting new potential biomarker in CRC management.
Hepatology
Stressed hepatocyte sustains alcohol-associated hepatitis progression by producing leukocyte cell-derived chemotaxin 2
Xu H, Wu Z, Qin J, et al. Stressed hepatocyte sustains alcohol-associated hepatitis progression by producing leukocyte cell-derived chemotaxin 2. Gut 2025; 74(8): 1321-1334. doi: 10.1136/gutjnl-2024-334318
Alcohol-associated hepatitis (AH) progression is driven by a deleterious interaction between hepatocytes and neutrophils mediated by hepatocyte-derived leucocyte cell–derived chemotaxin 2 (LECT2). Xu et al. analysed bulk and single-cell RNA sequencing data from AH patient liver tissues and demonstrated marked upregulation of LECT2, correlating strongly with disease severity. Clinical validation through serum measurements and biopsy assessments confirmed these findings. Further, Xu et al. found in ethanol-fed mouse models replicating human AH, hepatic LECT2 expression increased significantly, and pharmacological inhibition of endoplasmic reticulum stress abolished this induction. Genetic manipulations provided functional evidence: Lect2-deficient mice displayed markedly reduced liver injury following ethanol exposure, while hepatic overexpression of Lect2 exacerbated histological damage and biochemical markers of injury. Mechanistic studies demonstrated that LECT2 binds directly to prohibitin 2 (PHB2) on neutrophil membranes, destabilising PHB1/PHB2 heterodimers and triggering PHB2 degradation. This disruption promoted reactive oxygen species accumulation, neutrophil activation, and neutrophil extracellular trap formation, thereby perpetuating inflammatory damage. Therapeutic intervention using Lect2-targeted shRNA in vivo significantly ameliorated ethanol-induced liver injury, reducing neutrophil infiltration and inflammatory markers. Collectively, the findings reveal a pathogenic LECT2–PHB2 axis that establishes a self-perpetuating loop of hepatocyte–neutrophil crosstalk and sustained inflammation, driving AH progression. These findings may open new therapeutic avenue in AH by targeting LECT2, either by suppressing its expression through gene-silencing strategies, blocking its interaction with PHB2, or modulating upstream endoplasmic reticulum stress pathways.
Gene score to quantify systemic inflammation in patients with acutely decompensated cirrhosis
Trebicka J, Aguilar F, Queiroz Farias A, et al. Gene score to quantify systemic inflammation in patients with acutely decompensated cirrhosis. Gut 2025; 74(8):1293-1307. doi: 10.1136/gutjnl-2024-333876.
This study introduces and validates the CLIF-Systemic Inflammation Gene (CLIF-SIG) score, a novel transcriptomics-based biomarker for quantifying systemic inflammation (SI) in patients with acutely decompensated cirrhosis (ADC). Recognising the limitations of conventional biomarkers (e.g., CRP (C-reactive protein), WCC (white cell count), cytokines), Trebicka et al. analysed RNA-sequencing data from 700 hospitalised ADC patients across the PREDICT and ACLARA studies. A 28-gene signature reflecting immune cell-related expression changes was used to compute the CLIF-SIG score, stratifying patients by SI severity and prognosis.
The CLIF-SIG score significantly outperformed a composite of traditional biomarkers (CLIF-SBC) in differentiating patients with high-severity phenotypes (ACLF or early pre-ACLF) from those with lower severity. A threshold score of 0.386 (Youden Index) best predicted poor outcomes, with 80% of patients who developed ACLF during hospitalisation presenting above this cut-off. Importantly, the score’s predictive accuracy was consistent across liver disease aetiologies, demographics, and precipitating events.
Serial measurements revealed that SI in ADC progresses through distinct inflammatory phases, often beginning prior to hospitalisation. The score captured these dynamics and closely tracked 28- and 90-day mortality, independent of MELD-Na (Model for End-Stage Liver Disease – Sodium). Patients with persistent elevation of the CLIF-SIG score had the highest mortality risk.
Validation in external cohorts (including non-cirrhotic patients with sepsis or septic shock) confirmed the relevance of the 28-gene panel. Key contributors include genes involved in inflammasome activation (e.g., PYCARD (Apoptosis-associated speck-like protein containing a CARD)), macrophage activity (CD163 (Cluster of Differentiation 163)), and NK (natural killer) cell function (e.g., GZMH (Granzyme H), XCL1 (Chemokine (C motif) ligand 1)), aligning with known SI mechanisms in liver failure.
The CLIF-SIG score provides a more precise quantification of SI in ADC than current biomarkers. It has potential to improve patient stratification, guide immunomodulatory therapy, and monitor response longitudinally. While not yet ready for bedside use, development of rapid clinical assays is underway.
Stomach
Extracellular Vesicle–Derived lncRNA Signature Enables Early, Non-Invasive Detection of Early-Onset Gastric Cancer
Guo X, Wang W, Cheng X, et al. Diagnostic efficacy of an extracellular vesicle-derived lncRNA-based liquid biopsy signature for the early detection of early-onset gastric cancer. Gut 2025; 74(8): 1209-1218. doi: 10.1136/gutjnl-2024-333657.
Early-onset gastric cancer (EOGC), defined as gastric cancer occurring in individuals under 50 years old, carries high morbidity and often presents at an aggressive stage. Existing diagnostic biomarker, such as CEA (carcinoembryonic antigen), Helicobacter pylori serology, and pepsinogens, perform poorly in younger populations, and delayed detection can critically limit curative treatment options.
In this study, Guo et al. developed a non-invasive liquid biopsy signature based on three extracellular vesicle derived long non coding RNAs (EV lncRNAs): NALT1 (NOTCH1 Associated LncRNA In T Cell Acute Lymphoblastic Leukaemia 1), PTENP1 (Phosphatase and tensin homolog pseudogene 1), and HOTTIP (HOXA transcript at the distal tip). Through an integrated discovery phase using genome wide transcriptomics from tissue samples (43 EOGC, 31 late onset GC, and 37 controls), they identified candidate EV lncRNAs. These were then validated by qPCR across a large training cohort (299 patients) and two independent external validation cohorts (Xi’an, n=462; Beijing, n=438).
The three-component signature achieved strong diagnostic performance: AUC (area under the curve) = 0.924 (95% CI 0.889–0.953) in the training cohort and maintained high accuracy in both validation cohorts—AUC = 0.911 in Xi’an and AUC = 0.932 in Beijing. Importantly, the signature effectively identified resectable early stage (stage I/II) EOGCs from precancerous lesions, outperforming traditional biomarkers. Levels of these EV lncRNAs dropped after surgical resection, and were low or absent in other gastrointestinal cancers, supporting specificity to gastric cancer and responsiveness to tumour burden.
This EV lncRNA biomarker panel represents a promising, minimally invasive tool for early detection of EOGC, especially in resectable stages where curative treatment is possible. Guo et al. suggest potential clinical utility in screening young patients at risk, pending further prospective studies and broader validation.
Pancreas
Targeting MXD1 sensitises pancreatic cancer to trametinib
Zhang S, Deng S, Liu J, et al. Targeting MXD1 sensitises pancreatic cancer to trametinib. Gut 2025; 74(8): 1262-1278. doi: 10.1136/gutjnl-2024-333408.
Trametinib is an orally bioavailable mitogen-activated extracellular signal-regulated kinase 1 (MEK1) and MEK2 inhibitor. It was first approved for the treatment of melanoma, but its therapeutic potential is now being explored in other cancers, including pancreatic cancer. Initial trials for its use in Pancreatic ductal adenocarcinoma (PDAC) have not met with much success due to the development of drug resistance, which is considered multifactorial. In the present study, Zhang et al., aimed to address this issue using patient-derived xenograft models and multiomic analysis.
They found that trametinib-treated PDAC cells demonstrate resistance through viral mimicry. Many transposable elements (TEs) are overexpressed in PDAC cells treated with trametinib. Additionally, trametinib treatment leads to overexpression of MXD1 (MAX dimerisation protein 1) RNA and protein levels in trametinib-resistant PDAC cell lines. These results show that trametinib-induced MXD1 upregulation promotes TE transcription and dsRNA production, which activates viral mimicry in PDAC cells.
When MXD1 was depleted, PDAC proliferation decreased compared to control, and this effect was more pronounced when PDAC cells were treated with trametinib. These findings confirm that MXD1 may play a protumourigenic role, and its inhibition could help resolve the issue of trametinib resistance in PDAC. Further investigation revealed that PDAC xenografts (PDXs) treated with trametinib and MXD1 inhibitor showed sustained growth suppression, while those treated with trametinib plus control initially responded but later regrew due to resistance.
The targeted therapeutic response of PDAC to trametinib has been limited by drug resistance. The Zhang et al., discovered a potential mechanism for this resistance that could be exploited therapeutically. Hyperregulated viral mimicry, secondary to MXD1 upregulation, causes chromatin remodelling at TE loci, leading to trametinib resistance. The study also shows that inhibiting MXD1 restores trametinib-induced sustained tumour suppression. Moreover, MXD1 appears to act as a tumour promoter in PDAC, contrary to its previously assumed tumour-suppressive role.
Reviewers
Dr Benjamin Norton, Doctoral Research Student, Cleveland Clinic London (CCL) and University College London (UCL), London, UK
Dr Mohsen Subhani, Nottingham University Hospitals NHS Trust, Nottingham, UK
Dr Mie Thu Ko, NIHR ST4 Academic Clinical Fellow, University of East Anglia and Norfolk and Norwich University Hospital, Norwich, UK
Dr Benjamin Zare, St Mark’s National Bowel Hospital & Academic Institute, London, UK
Dr Ahmed El-Sayed, Clinical Research Fellow, UCL, London, UK
Dr Puneet Chhabra, Staff Specialist Gastroenterologist, Royal Hobart Hospital, Hobart, Tasmania, Australia
BSG GUT Highlights is edited by Dr Philip J Smith, Honorary Consultant Luminal Gastroenterologist, Royal Liverpool Hospital, Liverpool University Hospitals NHS Foundation Trust, Mount Vernon, Liverpool, UK. Dr Smith is the Digital and Education Editor of GUT, Editor in chief of Frontline Gastroenterology and Associate Editor of BMJ Open Gastroenterology.
Funding
The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.
Competing interests: None declared.
Provenance and peer review: Not commissioned; internally peer reviewed.