Microbiome and biofilm insights from normal vs tumor tissues in Thai colorectal cancer patients

Colorectal cancer (CRC) is a prevalent global malignancy with complex etiologies, including microbiota alterations. This study investigates gut microbiota and biofilm-producing bacteria in 35 Thai CRC patients, analyzing paired normal and tumor biopsy samples. Bacterial DNA from the V3-V4 region of 16S rRNA was sequenced, and biofilms were visualized via scanning electron microscopy and fluorescence in situ hybridization (FISH). Results revealed Firmicutes as the dominant phylum, followed by Bacteroidota, Proteobacteria, and Fusobacteriota, with Fusobacteriota and Bacteroidota notably enriched in left-sided CRC. Key biofilm producers-Bacteroides fragilis, Fusobacterium nucleatum, and Pasteurella stomatis-showed significantly higher gene expression in tumor tissues. Dense biofilms and higher Fusobacterium abundance, localized within the crypts of Lieberkuhn, were observed in CRC tissues. These findings highlight CRC-associated microbiota alterations and pathogenic biofilm production, emphasizing a spatial relationship between tumor location and microbial distribution, with potential implications for understanding CRC pathogenesis and therapeutic targeting.

Gut microbiome evolution from infancy to 8 years of age

The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.

Intratumoural pks+Escherichia coli is associated with risk of metachronous colorectal cancer and adenoma development in people with Lynch syndrome

BACKGROUND

The adverse gut microbiome may underlie the variability in risks of colorectal cancer (CRC) and metachronous CRC in people with Lynch syndrome (LS). The role of pks+/-Escherichia coli (pks+/-E. coli), Enterotoxigenic Bacteroides fragilis (ETBF), and Fusobacterium nucleatum (Fn) in CRCs and adenomas in people with LS is unknown.

METHODS

A total of 358 LS cases, including 386 CRCs, 90 adenomas, 195 normal colonic mucosa DNA from the Australasian Colon Cancer Family Registry were tested using multiplex TaqMan qPCR. Logistic regression was used to compare the intratumoural prevalence of each bacteria in Lynch CRCs with 1336 sporadic CRCs. Cox proportional-hazards regression estimated the associations of each bacteria with the risk of metachronous CRC and neoplasia.

FINDINGS

Pks+ E. coli (odds ratio [95% confidence interval] = 1.60 [1.08-2.35], P = 0.017), pks-E. coli (3.87 [2.58-5.80], P < 0.001) and Fn (19.47 [13.32-28.87], P < 0.001) were significantly enriched in LS CRCs when compared with sporadic CRCs. Pks+ E. coli in the initial CRC was associated with an increased risk of metachronous CRC (hazard ratio [95% confidence interval] = 2.32 [1.29-4.17], P = 0.005) and metachronous colorectal neoplasia (1.51 [1.02-2.23], P = 0.040) when compared with CRCs without pks+ E. coli.

INTERPRETATION

Pks+ E. coli, pks-E. coli, and Fn are enriched within LS CRCs, suggesting possible roles in CRC development in LS. Having intratumoural pks+ E. coli is associated with increased risk of metachronous CRC, suggesting that, if validated, people with LS might benefit from pks+ E. coli screening and eradication.

FUNDING

This work was funded by an NHMRC Investigator grant (GNT1194896) and a Cancer Australia/Cancer Council NSW co-funded grant (GNT2012914).

Gravitational forces and matrix stiffness modulate the invasiveness of breast cancer cells in bioprinted spheroids

The progression of breast cancer is influenced by the stiffness of the extracellular matrix (ECM), which becomes stiffer as cancer advances due to increased collagen IV and laminin secretion by cancer-associated fibroblasts. Intriguingly, breast cancer cells cultivated in two-dimensions exhibit a less aggressive behavior when exposed to weightlessness, or microgravity conditions. This study aims to elucidate the interplay between matrix stiffness and microgravity on breast cancer progression. For this purpose, three-dimensional spheroids of breast cancer cell lines (MCF-7 and MDA-MB-231) were formed. These spheroids were subsequently bioprinted in hydrogels of varying stiffness, obtained by the mixing of gelatin methacrylate and poly(ethylene) glycol diacrylate mixed at different ratios. The constructs were printed with a custom stereolithography (SLA) bioprinter converted from a low-cost, commercially available 3D printer. These bioprinted structures, encapsulating breast cancer spheroids, were then placed in a clinostat (microgravity simulation device) for a duration of seven days. Comparative analyses were conducted between objects cultured under microgravity and standard earth gravity conditions. Protein expression was characterized through fluorescent microscopy, while gene expression of MCF-7 constructs was analyzed via RNA sequencing. Remarkably, the influence of a stiffer ECM on the protein and gene expression levels of breast cancer cells could be modulated and sometimes even reversed in microgravity conditions. The study's findings hold implications for refining therapeutic strategies for advanced breast cancer stages - an array of genes involved in reversing aggressive or even metastatic behavior might lead to the discovery of new compounds that could be used in a clinical setting.

TRIM56 Promotes White Adipose Tissue Browning to Attenuate Obesity by Degrading TLE3

In mammals, the activation of thermogenic adipocytes, such as beige and brown adipocytes, can significantly increase overall energy expenditure, offering a promising strategy to combat metabolic diseases. Despite its considerable potential, the regulatory mechanisms governing this activation remain largely elusive. This study bridges this gap by elucidating that tripartite motif 56 (TRIM56), an E3 ubiquitin ligase, is upregulated in response to cold stimuli, thereby promoting the recruitment of beige adipocytes. Notably, the overexpression of TRIM56 in adipocytes is shown to help mice maintain a core temperature under cold conditions, as well as confer protection against diet-induced obesity. Mechanistically, TRIM56 facilitates the degradation of the transducin-like enhancer protein 3 (TLE3) protein by promoting its K48-linked ubiquitination, which subsequently triggers the activation of thermogenic genes in subcutaneousl white adipose tissue and improved the metabolic profiles. These findings unveil a novel function for TRIM56 in adipocyte browning, suggesting its potential as a therapeutic target for the treatment of metabolic disorders.

Systematic review: The gut microbiota as a link between colorectal cancer and obesity

Microbiome modulation is one of the novel strategies in medicine with the greatest future to improve the health of individuals and reduce the risk of different conditions, including metabolic, immune, inflammatory, and degenerative diseases, as well as cancer. Regarding the latter, many studies have reported the role of the gut microbiome in carcinogenesis, formation and progression of colorectal cancer (CRC), as well as its response to different systemic therapies. Likewise, obesity, one of the most important risk factors for CRC, is also well known for its association with gut dysbiosis. Moreover, obesity and CRC display, apart from microbial dysbiosis, chronic inflammation, which participates in their pathogenesis. Although human and murine studies demonstrate the significant impact of the microbiome in regulating energy metabolism and CRC development, little is understood about the contribution of the microbiome to the development of obesity-associated CRC. Therefore, this systematic review explores the evidence for microbiome changes associated with these conditions and hypothesizes that this may contribute to the pathogenesis of obesity-related CRC. Two databases were searched, and different studies on the relationship among obesity, intestinal microbiota and CRC in clinical and preclinical models were selected. Data extraction was carried out by two reviewers independently, and 101 studies were finally considered. Findings indicate the existence of a risk association between obesity and CRC derived from metabolic, immune, and microbial disorders.

Fecal Microbial Profiles and Short-Chain Fatty Acid/Bile Acid Metabolomics in Patients With Age-Related Macular Degeneration: A Pilot Study

Purpose

Age-related macular degeneration (AMD) is a multifactorial disease, and studies have implicated the role of gut microbiota in its pathogenesis. However, characterization of microbiome dysbiosis and associated microbial-derived metabolomic profiles across AMD stages remains unknown. In this pilot study, we explored how gut microbiome composition and gut-derived metabolites differ in AMD.

Methods

Our pilot study analyzed fasted stool samples that were collected from 22 patients at a tertiary academic center. Subjects were classified as control, intermediate AMD, or advanced AMD based on clinical presentation. 16S rRNA amplicon sequencing and standard chromatography-mass spectrometry methods were used to identify bacterial taxonomy composition and abundance of short-chain fatty acids (SCFAs) and bile acids (BAs), respectively. Genetic testing was used to investigate the frequency of 14 high-risk single nucleotide polymorphisms (SNPs) associated with AMD in the AMD cohort.

Results

Forty-three differentially abundant genera were present among the control, intermediate, and advanced groups. Taxa with known roles in immunologic pathways, such as Desulfovibrionales (q = 0.10) and Terrisporobacter (q = 1.16e-03), were in greater abundance in advanced AMD patients compared to intermediate. Advanced AMD patients had decreased abundance of 12 SCFAs, including acetate (P = 0.002), butyrate (P = 0.04), and propionate (P = 0.01), along with 12 BAs, including taurocholic acid (P = 0.02) and tauroursodeoxycholic acid (P = 0.04). Frequencies of high-risk SNPs were not significantly different between the intermediate and advanced AMD groups.

Conclusions

This pilot study identifies distinct gut microbiome compositions and metabolomic profiles associated with AMD and its stages, providing preliminary evidence of a potential link between gut microbiota and AMD pathogenesis. To validate these findings and elucidate the underlying mechanisms, future research with larger cohorts and more comprehensive sampling is strongly recommended.

Targeted editing of CCL5 with CRISPR-Cas9 nanoparticles enhances breast cancer immunotherapy

Breast cancer remains one of the leading causes of cancer-related mortality among women worldwide. Immunotherapy, a promising therapeutic approach, often faces challenges due to the immunosuppressive tumor microenvironment. This study explores the innovative use of CRISPR-Cas9 technology in conjunction with FCPCV nanoparticles to target and edit the C-C Motif Chemokine Ligand 5 (CCL5) gene, aiming to improve the efficacy of breast cancer immunotherapy. Single-cell RNA sequencing (scRNA-seq) and TCGA-BRCA data identified CCL5 as a key immune-related gene in breast cancer. Using CRISPR-Cas9, sgRNA targeting CCL5 was designed and delivered to breast cancer cells and humanized mouse models via FCPCV nanoparticles. In vitro experiments demonstrated that FCPCV nanoparticles effectively silenced CCL5, enhanced CD8+ T cell activity, and increased the production of cytokines such as IFN-γ, TNF-α, and GZMB. In vivo studies revealed significant tumor suppression, improved immune microenvironment, and increased CD8+/CD4+ ratios in treated mice, without notable toxic side effects. These findings highlight the potential of CRISPR-Cas9 nanoparticle-mediated gene editing as a novel strategy for enhancing breast cancer immunotherapy, providing a new direction for personalized and effective cancer treatment.

Regulation and application of m6A modification in tumor immunity

The m6A modification is an RNA modification that impacts various processes of RNA molecules, including transcription, splicing, stability, and translation. Recently, researchers have discovered that the presence of m6A modification can influence the interaction between tumor cells and immune cells and also play a role in regulating the expression of immune response-related genes. Additionally, m6A modification is intricately involved in the regulation of tumor immune evasion and drug resistance. Specifically, certain tumor cells can manipulate the gene expression through m6A modification to evade immune system attacks. Therefore, it might be possible to enhance tumor immune surveillance and improve the effectiveness of immune-based therapies by manipulating m6A modification. This review systematically discusses the role of m6A modification in tumor immunity, specifically highlighting its regulation of immune cells and immune-related genes in tumor cells. Furthermore, we explore the potential of m6A modification inhibitors as anti-cancer therapies and the significance of m6A regulatory factors in predicting the efficacy of tumor immune therapy.

A post-injury immune challenge with lipopolysaccharide following adult traumatic brain injury alters neuroinflammation and the gut microbiome acutely, but has little effect on chronic outcomes

Patients with a traumatic brain injury (TBI) are susceptible to hospital-acquired infections, presenting a significant challenge to an already-compromised immune system. The consequences and mechanisms by which this dual insult worsens outcomes are poorly understood. This study aimed to explore how a systemic immune stimulus (lipopolysaccharide, LPS) influences outcomes following experimental TBI in young adult mice. Male and female C57Bl/6J mice underwent controlled cortical impact or sham surgery, followed by 1 mg/kg i.p. LPS or saline-vehicle at 4 days post-TBI, before behavioral assessment and tissue collection at 6 h, 24 h, 7 days or 6 months. LPS induced acute sickness behaviors including weight loss, transient hypoactivity, and increased anxiety-like behavior. Early systemic immune activation by LPS was confirmed by increased spleen weight and serum cytokines. In brain tissue, gene expression analysis revealed a time course of inflammatory immune activation in TBI or LPS-treated mice (e.g., IL-1β, IL-6, CCL2, TNFα), which was exacerbated in TBI + LPS mice. This group also presented with fecal microbiome dysbiosis at 24 h post-LPS, with reduced bacterial diversity and changes in the relative abundance of key bacterial genera associated with sub-acute neurobehavioral and immune changes. Chronically, TBI induced hyperactivity and cognitive deficits, brain atrophy, and increased seizure susceptibility, similarly in vehicle and LPS-treated groups. Together, findings suggest that an immune challenge with LPS early after TBI, akin to a hospital-acquired infection, alters the acute neuroinflammatory response to injury, but has no lasting effects. Future studies could consider more clinically-relevant models of infection to build upon these findings.

Factors Affecting Liver Function Abnormalities After Laparoscopic Esophageal Hiatal Hernia Repair

OBJECTIVE

In this study, we investigated the factors related to abnormal liver function in patients undergoing laparoscopic esophageal hiatal hernia repair.

METHODS

The clinical data of 347 patients who underwent elective laparoscopic esophageal hiatal hernia repair at Beijing Chao-yang Hospital of Capital Medical University between January 2018 and November 2023 were retrospectively collected. The patients comprised 131 males and 216 females, ranging in age from 24 to 87 years, and were assessed using the ASA grading system between grades I and III. The patients were divided into 2 groups based on the presence or absence of liver function abnormalities on the first day after surgery: a normal liver function group (NLA group) and an abnormal liver function group (LA group). Patients with elevation in any of the following indicators were included in the LA group: alanine aminotransferase >40 U/L, glutamine aminotransferase >40 U/L, γ-glutamyltransferase >49 U/L, alkaline phosphatase >135 U/L, total bilirubin >17.1 μmol/L, or direct bilirubin >6.8 μmol/L. The clinical data of the 2 groups of patients were compared, and only the indicators with a P -value <0.15 were included in a binary logistic regression model analysis.

RESULTS

There were 238 patients (68.6%) who developed liver function abnormalities on the first postoperative day. In comparison to the NLA group, the LA group had a significantly higher proportion of patients with esophageal hiatal hernia type II, type III, and type IV, hypotension, and high P ET CO 2 . Furthermore, the LA group had a significantly lower proportion of patients receiving blood transfusions. The maximum length and maximum cross-sectional area of the esophageal hiatal hernia were also significantly larger in the LA group. In addition, the operation time was significantly longer in the LA group. (all P -values are <0.15). The binary logistic regression analysis revealed that prolonged operation time (OR=1.017, 95% CI: 1.007-1.028) was the only risk factor associated with postoperative liver function abnormalities.

CONCLUSIONS

The sole risk factor for postoperative liver function abnormalities was prolonged surgical time.

Gut Microbiota Modulation in IBD: From the Old Paradigm to Revolutionary Tools

Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders primarily comprising two main conditions: ulcerative colitis and Crohn's disease. The gut microbiota's role in driving inflammation in IBD has garnered significant attention, yet the precise mechanisms through which the microbiota influences IBD pathogenesis remain largely unclear. Given the limited therapeutic options for IBD, alternative microbiota-targeted therapies-including prebiotics, probiotics, postbiotics, and symbiotics-have been proposed. While these approaches have shown promising results, microbiota modulation is still mainly considered an adjunct therapy to conventional treatments, with a demonstrated impact on patients' quality of life. Fecal microbiota transplantation (FMT), already approved for treating Clostridioides difficile infection, represents the first in a series of innovative microbiota-based therapies under investigation. Microbial biotherapeutics are emerging as personalized and cutting-edge tools for IBD management, encompassing next-generation probiotics, bacterial consortia, bacteriophages, engineered probiotics, direct metabolic pathway modulation, and nanotherapeutics. This review explores microbial modulation as a therapeutic strategy for IBDs, highlighting current approaches and examining promising tools under development to better understand their potential clinical applications in managing intestinal inflammatory disorders.

The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures

BACKGROUND

The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.

METHODS

In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.

RESULTS

The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.698) and high-risk patients from controls (AUC = 0.761), and its predictive ability was also validated in external cohorts.

CONCLUSIONS

Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.

Antimicrobial resistance of pet-derived bacteria in China, 2000-2020

With the rapid growth of the pet industry in China, bacterial infectious diseases in pets have increased, highlighting the need to monitor antimicrobial resistance (AMR) in pet-derived bacteria to improve the diagnosis and treatment. Before the establishment of the China Antimicrobial Resistance Surveillance Network for Pets (CARPet) in 2021, a comprehensive analysis of such data in China was lacking. Our review of 38 point-prevalence surveys conducted between 2000 and 2020 revealed increasing trends in AMR among pet-derived Escherichia coli, Klebsiella pneumoniae, Staphylococcus spp., Enterococcus spp., and other bacterial pathogens in China. Notable resistance to β-lactams and fluoroquinolones, which are largely used in both pets and livestock animals, was observed. For example, resistance rates for ampicillin and ciprofloxacin in E. coli frequently exceeded 50.0%, with up to 41.3% of the isolates producing extended-spectrum β-lactamases. The emergence of carbapenem-resistant K. pneumoniae and E. coli, carrying blaNDM and blaOXA genes, highlighted the need for vigilant monitoring. The detection rate of SCCmec (Staphylococcal Cassette Chromosome mec), a genetic element associated with methicillin resistance, in Staphylococcus pseudintermedius isolated from pets in China was found to be over 40.0%. The resistance rate of E. faecalis to vancomycin was 2.1% (5/223) in East China, which was higher than the detection rate of human-derived vancomycin-resistant Enterococcus (0.1%, 12/11,215). Establishing the national AMR surveillance network CARPet was crucial, focusing on representative cities, diverse clinical samples, and including both commonly used antimicrobial agents in veterinary practice and critically important antimicrobial agents for human medicine, such as carbapenems, tigecycline, and vancomycin.

Fecal microbiota transplantation: application scenarios, efficacy prediction, and factors impacting donor-recipient interplay

Fecal microbiota transplantation (FMT) represents a therapeutic approach that directly regulates the gut microbiota of recipients, normalizes its composition and reaping therapeutic rewards. Currently, in addition to its general application in treating Clostridium difficile (C. difficile) infection (CDI), FMT treatment has also been extended to the fields of other gastrointestinal diseases, infections, gut-liver or gut-brain axis disorders, metabolic diseases and cancer, etc. Prior to FMT, rigorous donor screening is essential to reduce the occurrence of adverse events. In addition, it is imperative to evaluate whether the recipient can safely and effectively undergo FMT treatment. However, the efficacy of FMT is influenced by the complex interactions between the gut microbiota of donor and recipient, the degree of donor microbiota engraftment is not necessarily positively related with the success rate of FMT. Furthermore, an increasing number of novel factors affecting FMT outcomes are being identified in recent clinical trials and animal experiments, broadening our understanding of FMT treatment. This article provides a comprehensive review of the application scenarios of FMT, the factors influencing the safety and efficacy of FMT from the aspects of both the donors and the recipients, and summarizes how these emerging novel regulatory factors can be combined to predict the clinical outcomes of patients undergoing FMT.

Proteus mirabilis exacerbates ulcerative colitis by inhibiting mucin production

Introduction

Ulcerative colitis (UC) is characterized by chronic inflammation and ulceration in colonic mucosa, accompanied by a defective epithelial barrier. Proteus mirabilis (P. mirabilis) bacterium is a putative intestinal pathogen with invasive ability, yet its role in UC inflammation and gut barrier disruption is unclear. This study aims to investigate its epidemiological presence, pathogenic roles and preventive strategy during UC inflammation.

Method

P. mirabilis culture and PCR amplification of the P. mirabilis-specific ureR gene were used to detect fecal P. mirabilis and determine its prevalence in UC and control stool specimens. P. mirabilis isolated from UC stool specimens was gavaged into dextran sulfate sodium (DSS)-treated mice. Inflammation and the mucus layer of colons were assessed through histological examination and cytokine quantification. Bacteriophages were screened and used to eliminate P. mirabilis in colitis animals.

Results and discussion

The fecal P. mirabilis bacteria were detected by PCR amplification of P. mirabilis-specific ureR gene. Of 41 UC patients, 65.9% patients were P. mirabilis positive, which was significantly higher than the controls. Administration of P. mirabilis aggravated DSS-induced colitis symptom and mucosal inflammation in mice. Interestingly, the colonic mucus layer, an essential component of the epithelial barrier, of the animals was dramatically disrupted, which was consistent with the alteration of human UC colon. The disrupted mucus layer was mediated by the down-regulation of IL-18 in intestinal epithelium. Importantly, a bacteriophage cocktail targeting P. mirabilis could restore the mucus barrier and alleviate the enteric inflammation. Thus, our results suggest that P. mirabilis is a UC pathobiont bacterium, which exacerbates the severity of UC inflammation owing to down-regulation of mucin production and IL-18 expression. Bacteriophage-mediated elimination of P. mirabilis may be effective in limiting UC inflammation.

Fu Brick Tea Protects the Intestinal Barrier and Ameliorates Colitis in Mice by Regulating Gut Microbiota

Ulcerative colitis (UC) pathogenesis is strongly linked to gut microbiota dysbiosis and compromised intestinal barrier integrity. Emerging evidence suggests that targeted dietary interventions may restore microbial homeostasis and ameliorate colitis progression. In this study, we evaluated the therapeutic potential of Fu Brick tea (FBT) using a dextran sulfate sodium (DSS)-induced murine colitis model. The results indicated that oral administration of FBT extract significantly improved the disease index, reduced inflammatory response, protected intestinal barrier protein (e.g., ZO-1), and maintained intestinal structure integrity. Furthermore, FBT intake increased the diversity of gut microbiota, promoted the growth of beneficial bacteria (e.g., Akkermansia), inhibited the proliferation of harmful bacteria (e.g., Desulfovibrioceae, Escherichia, and Helicobacter), restored intestinal homeostasis, and alleviated colitis symptoms including diarrhea. These findings position FBT as a promising nutraceutical candidate for UC management via multi-target modulation of mucosal immunity and microbial ecology.

Sex Differences Outweigh Dietary Factors in Food-Related Quality of Life in Patients with Inflammatory Bowel Disease

BACKGROUND

Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), consists of chronic gastrointestinal inflammation, with nutrition playing a significant role in its development. IBD patients often face dietary challenges affecting their quality of life (QoL), yet research on food-related QoL (FR-QoL) and sex-specific differences is limited. It was hypothesized that dietary patterns and choices impact food-related quality of life in IBD and that these effects vary by sex. The objective of this analysis was, therefore, to evaluate the impact of diet on food-related quality of life for men and women with IBD, respectively.

METHODS

A monocentric, cross-sectional study at a tertiary referral center analyzed the food-related quality of life in 117 women and 116 men with IBD, with a particular focus on dietary choices and patterns. To achieve this, multiple assessment tools, including the German version of the IBD-specific Questionnaire for Food-Related Quality of Life (FR-QoL-29-German) and a validated Food Frequency Questionnaire (FFQ) for dietary behavior, were used. Clinical indices (Harvey-Bradshaw Index (HBI); Partial Mayo Score (PMS)) and biochemical markers (C-reactive protein; fecal calprotectin) were evaluated.

RESULTS

The FR-QoL-29-German sum score differed significantly between the sexes (p = 0.034; g = -0.3), with men showing a higher mean score. Distinct dietary patterns showed little correlation with FR-QoL for both sexes, except for a significant inverse correlation between FR-QoL and sQ-HPF scores for men (p = 0.021; r = -0.214) but not for women (p = 0.897; r = -0.012). In a logistic regression analysis that was adjusted for confounding, the impact of IBD-specific and diet-related factors on FR-QoL was assessed, and disease entity was identified as a significant influencing factor for men but not for women. In women, older age and lower body weight were associated with higher FR-QoL.

CONCLUSIONS

The findings of this study indicate that dietary choices and patterns do not exhibit uniform associations with IBD-related quality of life. In addition, sex differences have been identified as a substantial factor in IBD food-related quality of life.

Pediatric Inflammatory Bowel Disease in Romania: The First Epidemiological Study of the North-West Region (2000-2020)

Background: Inflammatory bowel disease (IBD) represents a group of disorders with increasing incidence in the pediatric population worldwide. There are limited data on pediatric IBD (pIBD) epidemiology in Eastern Europe and none so far from Romania. The aim of our study was to evaluate incidence rates and time trends for pIBD in the north-west region of Romania and to compare them with results from studies on the same topic published worldwide. Methods: We performed a retrospective study of patients under 18 years of age diagnosed with pIBD in the time frame between 1 January 2000 and 31 December 2020 at the Emergency Clinical Hospital for Children in Cluj-Napoca. Age-adjusted incidence rates, annual percentage change (APC), average annual percentage chance (AAPC) and their corresponding 95% confidence intervals (CIs) were calculated for pIBD, Crohn's disease (CD) and ulcerative colitis (UC). Temporal trends were plotted using Joinpoint regression. Results: Ninety-four patients were identified. For the entire studied period, the incidence rate for pIBD was 0.79/105 (±0.74), 0.4/105 for CD (±0.42) and 0.34/105 for UC (±0.4). Time trends for incidence were positive, but statistical significance was found only for pIBD and CD. The APC observed for pIBD, CD and UC was 12 (95% CI: 6.5-17.7), 13.1 (95% CI: 8-18.5) and 5.67 (95% CI: 1.5-13.4), respectively. Comparison to other similar studies placed Romania among the countries with the lowest incidence of pIBD. Conclusions: Although pIBD incidence in our region appears to be low, there has been an important and significant increase in the incidence of overall pIBD and especially CD.

Design and synthesis of terephthalic dihydrazide analogues as dual inhibitors of glycation and urease

The overexpression of urease is the root cause of peptic ulcers and gastritis. Therefore, introducing new inhibitors against urease is a possible therapeutic approach to overcoming the pathogenesis; for instance, limiting the risk of development of urinary calculi. Moreover, glycation is the leading cause of several complications. Thus, in this study, we synthesized novel terephthalic dihydrazide analogues and evaluated their biological importance. These terephthalic dihydrazide analogues were characterized using advanced spectroscopic techniques, such as 1H NMR, 13C NMR, 19F NMR and HRMS (ESI+), and FT-IR. Fortunately, 6 of the 11 synthesized compounds exhibited urease inhibitory capability, and 8 compounds exhibited anti-glycation capability. Compounds 13-14, 20 and 23 showed significant urease inhibition with IC50 values of 63.12 ± 0.28, 65.71 ± 0.40, 49.2 ± 0.49 and 51.45 ± 0.39 μM, respectively. Meanwhile, they exhibited potent anti-glycation activity with IC50 values of 67.53 ± 0.46, 68.06 ± 0.43, 48.32 ± 0.42 and 54.36 ± 0.40 μM, respectively. Molecular docking of active urease inhibitors showed their good binding at the entrance of the active site and good correlation with our in vitro results.

Beckwith-Wiedemann syndrome and large offspring syndrome involve alterations in methylome, transcriptome, and chromatin configuration

Beckwith-Wiedemann Syndrome (BWS) is the most common epigenetic overgrowth syndrome, caused by epigenetic alterations on chromosome 11p15. In ∼50% of patients with BWS, the imprinted region KvDMR1 (IC2) is hypomethylated. Nearly all children with BWS develop organ overgrowth and up to 28% develop cancer during childhood. The global epigenetic alterations beyond the 11p15 region in BWS are not currently known. Uncovering these alterations at the methylome, transcriptome, and chromatin architecture levels are necessary steps to improve the diagnosis and understanding of patients with BWS. Here we characterized the complete epigenetic profiles of BWS IC2 individuals together with the animal model of BWS, bovine large offspring syndrome (LOS). A novel finding of this research is the identification of two molecular subgroups of BWS IC2 individuals. Genome-wide alternations were detected for DNA methylation, transcript abundance, alternative splicing events of RNA, chromosome compartments, and topologically associating domains (TADs) in BWS and LOS, with shared alterations identified between species. Altered chromosome compartments and TADs were correlated with differentially expressed genes in BWS and LOS. Together, we highlight genes and genomic regions that have the potential to serve as targets for biomarker development to improve current molecular diagnostic methodologies for BWS.

Machine Learning and Artificial Intelligence in the Multi-Omics Approach to Gut Microbiota

The gut microbiome is involved in human health and disease, and its comprehensive understanding is necessary to exploit it as a diagnostic or therapeutic tool. Multi-omics approaches, including metagenomics, metatranscriptomics, metabolomics, and metaproteomics, enable depiction of the gut microbial ecosystem's complexity. However, these tools generate a large data stream in which integration is needed to produce clinically useful readouts, but, in turn, might be difficult to carry out with conventional statistical methods. Artificial intelligence and machine learning have been increasingly applied to multi-omics datasets in several conditions associated with microbiome disruption, from chronic disorders to cancer. Such tools have potential for clinical implementation, including discovery of microbial biomarkers for disease classification or prediction, prediction of response to specific treatments, and fine-tuning of microbiome-modulating therapies. The state of the art, potential, and limits, of artificial intelligence and machine learning in the multi-omics approach to gut microbiome are discussed.

Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts

Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.

The influence of the microbiome on radiotherapy and DNA damage responses

Colorectal cancer (CRC) is one of the most prevalent cancers in terms of diagnosis and mortality. Radiotherapy (RT) remains a mainstay of CRC therapy. As RT relies on DNA damage to promote tumor cell death, the activity of cellular DNA damage repair pathways can modulate cancer sensitivity to therapy. The gut microbiome has been shown to influence intestinal health and is independently associated with CRC development, treatment responses and outcomes. The microbiome can also modulate responses to CRC RT through various mechanisms such as community structure, toxins and metabolites. In this review we explore the use of RT in the treatment of CRC and the molecular factors that influence treatment outcomes. We also discuss how the microbiome can promote radiosensitivity versus radioprotection to modulate RT outcomes in CRC. Understanding the molecular interaction between the microbiome and DNA repair pathways can assist with predicting responses to RT. Once described, these connections between the microbiome and RT response can also be used to identify actionable targets for therapeutic development.

Advances in gut microbiota-related treatment strategies for managing colorectal cancer in humans

Colorectal cancer (CRC) is a major contributor to global cancer-related mortality with increasing incidence rates in both developed and developing regions. Therefore, CRC presents a significant challenge to global health. The development of innovative tools for enhancing early CRC screening and diagnosis, along with novel treatments and therapies for improved management, remains an urgent necessity. CRC is intricately associated with the gut microbiota, which is integral to food digestion, nutrient generation, drug metabolism, metabolite production, immune enhancement, endocrine regulation, neurogenesis modulation, and the maintenance of physiologic and psychological equilibrium. Dysbiosis or imbalances in the gut microbiome have been implicated in various disorders, including CRC. Emerging evidence highlights the critical role of the gut microbiome in CRC pathogenesis and treatment, which presents potential opportunities for early detection and diagnosis. Despite substantial advances in understanding the relationship between the gut microbiota and CRC, significant challenges persist. Gaining a deeper and more detailed understanding of the interactions between the human microbiota and cancer is essential to fully realize the potential of the microbiota in cancer management. Unlike genetic factors, the gut microbiome is subject to modification, offering a promising avenue for the development of CRC treatments and drug discovery. This review provides an overview of the interactions between the human gut microbiome and CRC, while examining prospects for precision management of CRC.

Gut Microbiota Serves as a Crucial Independent Biomarker in Inflammatory Bowel Disease (IBD)

Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD), ulcerative colitis (UC), and IBD unclassified (IBD-U), is a complex intestinal disorder influenced by genetic, environmental, and microbial factors. Recent evidence highlights the gut microbiota as a pivotal biomarker and modulator in IBD pathogenesis. Dysbiosis, characterized by reduced microbial diversity and altered composition, is a hallmark of IBD. A consistent decrease in anti-inflammatory bacteria, such as Faecalibacterium prausnitzii, and an increase in pro-inflammatory species, including Escherichia coli, have been observed. Metabolomic studies reveal decreased short-chain fatty acids (SCFAs) and secondary bile acids, critical for gut homeostasis, alongside elevated pro-inflammatory metabolites. The gut microbiota interacts with host immune pathways, influencing morphogens, glycosylation, and podoplanin (PDPN) expression. The disruption of glycosylation impairs mucosal barriers, while aberrant PDPN activity exacerbates inflammation. Additionally, microbial alterations contribute to oxidative stress, further destabilizing intestinal barriers. These molecular and cellular disruptions underscore the role of the microbiome in IBD pathophysiology. Emerging therapeutic strategies, including probiotics, prebiotics, and dietary interventions, aim to restore microbial balance and mitigate inflammation. Advanced studies on microbiota-targeted therapies reveal their potential to reduce disease severity and improve patient outcomes. Nevertheless, further research is needed to elucidate the bidirectional interactions between the gut microbiome and host immune responses and to translate these insights into clinical applications. This review consolidates current findings on the gut microbiota's role in IBD, emphasizing its diagnostic and therapeutic implications, and advocates for the continued exploration of microbiome-based interventions to combat this debilitating disease.

RNF6 promotes cell proliferation of glioblastoma by targeting ubiquitin-mediated degradation of p27

RNF6 (RING finger protein 6), an atypical RING-type ubiquitin ligase, has been reported to be a potential tumor promoter in several human cancers. However, the role of RNF6 in glioblastoma remains poorly understood. In this study, we found that RNF6 was highly expressed in glioblastoma tissues, and its elevated expression was significantly associated with poor prognosis in glioblastoma patients. RNF6 depletion remarkably inhibited cell growth of glioblastoma cells. Mechanistically, RNF6 depletion stabilized p27 protein expression. We demonstrated that RNF6 interacted with p27 and mediated its ubiquitination and degradation in an E3 ligase activity-dependent manner. Moreover, we provide the first evidence revealing the crucial role RNF6 in mediating SKP2 expression at both transcriptional and post-translational levels. On the one hand, RNF6 played as a transcription factor to regulate the activity of the SKP2 promoter. On the other hand, RNF6 interacted with SKP2 and stabilized its protein levels in an Akt-dependent manner. Collectively, our data indicated that RNF6 accelerated glioblastoma cell proliferation and tumorigenesis by targeting p27 for degradation.

Impacts of ribosomal RNA sequence variation on gene expression and phenotype

Since the framing of the Central Dogma, it has been speculated that physically distinct ribosomes within cells may influence gene expression and cellular physiology. While heterogeneity in ribosome composition has been reported in bacteria, protozoans, fungi, zebrafish, mice and humans, its functional implications remain actively debated. Here, we review recent evidence demonstrating that expression of conserved variant ribosomal DNA (rDNA) alleles in bacteria, mice and humans renders their actively translating ribosome pool intrinsically heterogeneous at the level of ribosomal RNA (rRNA). In this context, we discuss reports that nutrient limitation-induced stress in Escherichia coli leads to changes in variant rRNA allele expression, programmatically altering transcription and cellular phenotype. We highlight that cells expressing ribosomes from distinct operons exhibit distinct drug sensitivities, which can be recapitulated in vitro and potentially rationalized by subtle perturbations in ribosome structure or in their dynamic properties. Finally, we discuss evidence that differential expression of variant rDNA alleles results in different populations of ribosome subtypes within mammalian tissues. These findings motivate further research into the impacts of rRNA heterogeneities on ribosomal function and predict that strategies targeting distinct ribosome subtypes may hold therapeutic potential.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.

Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial

BACKGROUND

Clinical data on oral fecal microbiota transplantation (FMT), a promising therapy for Crohn's disease (CD), are limited. Herein, we determined the short-term safety and feasibility of FMT for pediatric patients with active CD.

METHODS

In this open-label, parallel-group, single-center prospective trial, patients with active CD were treated with oral FMT capsules combined with partial enteral nutrition (PEN) (80%). The control group comprised pediatric patients with active CD treated with PEN (80%) and immunosuppressants. Thirty-three patients (11.6 ± 1.82 years)-17 in the capsule and 16 in the control groups-were analyzed. Data regarding the adverse events, clinical reactions, intestinal microbiome composition, and biomarker parameters were collected and compared post-treatment.

RESULTS

At week 10, the clinical and endoscopic remission rates did not differ between the two groups. By week 10, the mean fecal calprotectin level, C-reactive protein level, erythrocyte sedimentation rate, simple endoscopic score for CD, and pediatric CD activity index decreased significantly in the capsule group (all P < 0.05). The main adverse event was mild-to-moderate constipation. Core functional genera, Agathobacter, Akkermansia, Roseburia, Blautia, Subdoligranulum, and Faecalibacterium, were lacking pre-treatment. Post-treatment, the implantation rates of these core functional genera increased significantly, which positively correlated with the anti-inflammatory factor, interleukin (IL)-10, and negatively correlated with the pro-inflammatory factor, IL-6. The combination of these six functional genera distinguished healthy children from those with CD (area under the curve = 0.96).

CONCLUSIONS

Oral FMT capsules combined with PEN (80%) could be an effective therapy for children with active CD. The six core functional genera identified here may be candidate biomarkers for identifying children with CD.

TRIAL REGISTRATION

ClinicalTrials.gov, retrospectively registered, ID# NCT05321758, NCT05321745, date of registration: 2022-04-04.

A transcriptomic score to classify the inflammation-dysplasia-cancer sequence lesions in inflammatory bowel disease

BACKGROUND AND AIMS

Inflammatory bowel disease (IBD) is associated with a higher risk of developing colorectal cancer, according to the inflammation-dysplasia-cancer (IDC) sequence from inflammation to colitis-associated colorectal cancer (CAC). The objective of this study was to identify and generate a transcriptomic signature and score, related to the IDC sequence, that could ultimately classify dysplasia and cancer in IBD.

METHODS

Demographics, clinical parameters, histological characteristics, and RNA-sequencing data were evaluated on 134 formalin-fixed paraffin-embedded lesions from 2 independent cohorts of IBD patients with low- or high-grade dysplasia (LGD, HGD) and/or CAC. An ordinal logistic regression screened for significant IDC sequence-associated genes that were computed in a transcriptomic signature score.

RESULTS

Principal component analysis and unsupervised clustering on 1% of the most variable genes showed a good clustering between the 4 lesion groups (Normal Mucosa, Inflamed Mucosa, LGD/HGD, and CAC). A gene signature was identified on 27 genes that correlated with the lesion groups in the exploratory cohort. The most weighted gene in this transcriptomic signature was the long non-coding regulatory RNA KCNQ1OT1, a gatekeeper against genomic instability and transposon activation. Based on the expression of these 27 genes, we built and validated a transcriptomic signature score to classify dysplasia and CAC. The overall accuracy of the transcriptomic signature score was 85.71% in the exploratory cohort and 90.91% in the validation cohort.

CONCLUSION

We identified a tissue-based transcriptomic score to classify IDC lesions in IBD patients and uncovered some of the pivotal genes in carcinogenesis related to inflammation in IBD.

Untargeted Metabolomic Profiling of Colonic Mucosa in Individuals with Irritable Bowel Syndrome

Background: Irritable Bowel Syndrome (IBS) is a complex disorder characterized by altered gut-brain interactions, with gastrointestinal microbiota and metabolic dysregulation playing key roles in its pathophysiology. Identifying specific metabolic alterations within the colonic mucosa may enhance our understanding of IBS and contribute to improved diagnostic and therapeutic approaches. Methods: This cross-sectional study analyzed the metabolomic profiles of colonic mucosal biopsies from 44 IBS patients assessed with ROME IV criteria and 69 healthy controls undergoing colonoscopy. Untargeted metabolomic profiling was conducted using liquid chromatography-mass spectrometry (LC-MS), and differential metabolite analysis was performed via fold-change calculations and machine learning-based classification. Results: IBS patients exhibited distinct mucosal metabolic profiles, with significantly elevated levels of N-acetylneuraminic acid and 1-palmitoylglycerol, suggesting compromised epithelial integrity and increased gut permeability. In contrast, cis-4-hydroxycyclohexanecarboxylic acid, a metabolite associated with protective mucosal functions, was reduced. Random Forest analysis identified these metabolites as key discriminatory features between IBS and control groups, reinforcing their potential role as biomarkers for IBS-related mucosal alterations. Conclusions: Our study highlights the unique metabolomic signatures of IBS at the mucosal level, emphasizing the role of microbial metabolites in disease pathology. These findings may facilitate the development of novel diagnostic tools and targeted therapeutic strategies, advancing personalized management for IBS patients.

Transcriptional and microbial profile of gastric cancer patients infected with Epstein-Barr virus

Introduction

Gastric cancer (GC), which has low survival rates and high mortality, is a major concern, particularly in Asia and South America, with over one million annual cases. Epstein-Barr virus (EBV) is recognized as a carcinogen that may trigger gastric carcinogenesis by infecting the stomach epithelium via reactivated B cells, with growing evidence linking it to GC. This study investigates the transcriptional and microbial profiles of EBV-infected versus EBV-non-infected GC patients.

Methods

Using Illumina NextSeq, cDNA libraries were sequenced, and reads were aligned to the human genome and analyzed with DESeq2. Kegg and differential analyses revealed key genes and pathways. Gene sensitivity and specificity were assessed using ROC curves (p < 0.05, AUC > 0.8). Non-aligned reads were used for microbiome analysis with Kraken2 for bacterial identification. Microbial analysis included LDA score, Alpha and Beta diversity metrics, with significance set at p ≤ 0.05. Spearman's correlation between differentially expressed genes (DEGs) and bacteria were also examined.

Results

The data revealed a gene expression pattern in EBV-positive gastric cancer, highlighting immune response, inflammation, and cell proliferation genes (e.g., GBP4, ICAM1, IL32, TNFSF10). ROC analysis identified genes with high specificity and sensitivity for discriminating EBV+ gastric cancer, including GBP5, CMKLR1, GM2A and CXCL11 that play pivotal roles in immune response, inflammation, and cancer. Functional enrichment pointed to cytokine-cytokine receptor interactions, antigen processing, and Th17 immune response, emphasizing the role of the tumor microenvironment, shaped by inflammation and immunomodulation, in EBV-associated GC. Microbial analysis revealed changes in the gastric microbiota in EBV+ samples, with a significant reduction in bacterial taxa. The genera Choristoneura and Bartonella were more abundant in EBV+ GC, while more abundant bacteria in EBV- GC included Citrobacter, Acidithiobacillus and Biochmannia. Spearman's correlation showed a strong link between DE bacterial genera and DEGs involved in processes like cell differentiation, cytokine production, digestion, and cell death.

Conclusion

These findings suggest a complex interaction between the host (EBV+ GC) and the microbiota, possibly influencing cancer progression, and offering potential therapeutic targets such as microbiota modulation or gene regulation. Comparing with EBV- samples further highlights the specific impact of EBV and the microbiota on gastric cancer pathogenesis.

Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach

Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases.

Ethacrynic acid inhibits the growth and proliferation of prostate cancer cells by targeting GSTP1 and regulating the PI3K-AKT signaling pathway

BACKGROUND

As a diuretic, ethacrynic acid (EA) has been shown to play a suppressive role in cancers, including prostate cancer (PC). However, its molecular regulatory mechanism is still unclear. Therefore, our study is centered on investigating the effect of EA on PC development and its mechanism.

METHODS

To verify the binding relationship between EA and GSTP1, molecular docking and cellular thermal shift assay (CETSA) were conducted. To examine how EA affects PC cell proliferation, cell cycle, and apoptosis, cell function assays were performed. qRT-PCR was used to detect GSTP1 mRNA expression. The expression of GSTP1 protein and PI3K-AKT signaling pathway-related proteins in cells was detected by western blot (WB). To verify how EA and GSTP1 influence cell growth in PC, in vivo experiments were conducted.

RESULTS

The binding relationship between GSTP1 and EA was confirmed by molecular docking and CETSA results. Cell experiments showed that EA could hinder PI3K/AKT pathway and PC cell proliferation, arrest the cell cycle in G0/G1 phase, and facilitate apoptosis by binding to GSTP1. In vivo experiments in nude mice verified that the interaction between EA and GSTP1 reduced PI3K and AKT phosphorylation and inhibited the growth of PC cells.

CONCLUSION

EA inhibits PC progression by binding to GSTP1 to downregulate the activity of PI3K/AKT pathway, and this result suggests the potential of EA to be an anticancer agent for PC therapy.

OSR1 suppresses oral squamous cell carcinoma proliferation and migration via the AXIN2/β-catenin pathway

OBJECTIVES

The odd-skipped related transcription factor 1 (OSR1) gene exerts distinct regulatory effects on tumorigenesis and development in various cancer types. However, the precise role of OSR1 in oral squamous cell carcinoma (OSCC) remains to be elucidated.

METHODS

GEPIA 2 and TCGA databases were utilized to analyze the OSR1 expression in head and neck squamous cell carcinoma (HNSC) patients and its impact on prognosis. Hematoxylin-eosin staining, immunohistochemistry, immunofluorescence, western blotting, and RT-qPCR were employed to detect the OSR1 expression in OSCC tissues and cells. Lentivirus transfection was utilized for overexpression and downexpression of OSR1 in OSCC. CCK8 cell proliferation assay, colony formation and cell scratch assay were conducted to investigate the effects of OSR1 on biological behavior of OSCC cells. Western blotting and RT-qPCR were applied to investigate the regulatory mechanism of OSR1 on AXIN2/β-catenin signaling pathway.

RESULTS

OSR1 expression was significantly decreased in HNSC patients, OSCC tissues and cells, leading to a decrease in 5-year survival rate. OSR1 overexpression inhibited the proliferation and migration of OSCC cells, and the AXIN2/β-catenin signaling pathway was inhibited. Silencing OSR1 had the opposite effect.

CONCLUSIONS

OSR1 functioned as a tumor suppressor gene in OSCC proliferation and migration by regulating the AXIN2/β-catenin signaling pathway.

The Prognostic Value of Tumor-Associated Neutrophils in Colorectal Cancer: A Systematic Review and Meta-Analysis

BACKGROUND

Tumor-associated neutrophils (TANs) are important components of the colorectal cancer (CRC) microenvironment. However, their role in CRC remains controversial. This study aimed to assess the prognostic value of TANs in patients with CRC.

METHODS

We searched the PubMed, EMBASE, and Cochrane Library databases for eligible studies published until January 9, 2023. The pooled hazard ratios (HRs) and odds ratios (ORs) with their 95% confidence intervals (95% CI) were calculated with a random-effects model to assess survival outcomes and clinicopathological features. Subgroup analyses were further conducted to identify potential sources of heterogeneity. Funnel plots and Egger's test were used to measure publication bias.

RESULTS

A total of 19 studies with 7721 patients were included in this meta-analysis. The pooled analysis indicated that high peritumoral TAN infiltration in CRC tissue was significantly associated with favorable cancer-specific survival (HR = 0.57; 95% CI: 0.38-0.86; p = 0.007), but not with overall survival or disease-free survival. No association between high intratumoral or unclear compartment TAN infiltration and CRC prognosis was found. Subgroup analyses showed that the association between TANs and the prognosis of CRC patients differed according to antibody types, tumor stage, quantitative methods, and follow-up time. High intratumoral TAN infiltration was significantly associated with histology type, whereas high TAN infiltration in an unclear compartment was significantly associated with gender, tumor location, and the primary tumor site.

CONCLUSIONS

High TAN infiltration, especially in the peritumoral compartment, could be a potential prognostic marker in CRC. More high-quality studies are required to explore its specific prognostic value in CRC.

The Lived Experience of Adults With Inflammatory Bowel Disease in Rural Areas: Phenomenological Study

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic gastrointestinal condition with a multifactorial etiology. It significantly impacts patients' quality of life, particularly, in rural areas where access to specialized care is limited. Challenges such as increased travel costs, social isolation, and restricted healthcare access are recognized, but their specific impact on rural Italian patients remains underexplored. This study aims to fill this gap. Using Cohen's hermeneutic phenomenological approach, in-depth interviews were conducted with 17 IBD patients from rural areas. Thematic analysis identified key patterns and themes. Two main themes emerged: "challenges of rural living," including economic concerns and social isolation, and "communication that bridges distances." Rural IBD patients face unique challenges extending beyond disease management, with economic hardship and social isolation being prominent. These findings highlight the need for tailored interventions to bridge healthcare gaps and improve the quality of life for rural patients, offering novel insights into their lived experiences in Italy.

Nanosize Non-Viral Gene Therapy Reverses Senescence Reprograming Driven by PBRM1 Deficiency to Suppress iCCA Progression

Polybromo-1 (PBRM1) serves as a crucial regulator of gene transcription in various tumors, including intrahepatic cholangiocarcinoma (iCCA). However, the exact role of PBRM1 in iCCA and the mechanism by which it regulates downstream target genes remain unclear. This research has revealed that PBRM1 is significantly downregulated in iCCA tissues, and this reduced expression is linked to aggressive clinicopathological features and a poor prognosis. Furthermore, it is demonstrated that PBRM1 can impede iCCA progression, and a gene therapy nanomedicine is developed to treat iCCA in vivo by modulating PBRM1 expression. The heightened expression of PBRM1 induces by the nanomedicine substantially inhibited tumor growth in iCCA. Conversely, the decrease in PBRM1 results in the abnormal activation of the ERK1/2 signaling pathway, a reduction in p16, p53/p21, and cellular senescence, thereby promoting iCCA advancement. Treatment with U0126, an ERK1/2 inhibitor, effectively halted iCCA progression by regulating the PBRM1-ERK1/2-cellular senescence pathway. These findings underscore the significant role of PBRM1 in controlling iCCA progression and predicting prognosis. Targeting the PBRM1-ERK1/2-cellular senescence pathway with U0126 shows promise for clinical applications in treating iCCA.

Repurposing thioridazine as a potential CD2068 inhibitor to mitigate antibiotic resistance in Clostridioides difficile infection

Clostridioides difficile infection (CDI) is a major public health issue, driven by antibiotic resistance and frequent recurrence. CD2068, an ABC protein in C. difficile, is associated with drug resistance, making it a potential target for novel therapies. This study explored FDA-approved non-antibiotic drugs for their ability to inhibit CD2068 through drug screening and experimental validation. Thioridazine exhibited moderate binding affinity to CD2068 and inhibited its ATP hydrolysis activity. It also suppressed the growth of multiple C. difficile ribotypes at 64-128 µg/mL, with rapid-killing effects. When combined with sub-MIC levels of standard antibiotics, thioridazine significantly reduced bacterial growth. In a mouse CDI model, thioridazine demonstrated potential in restoring gut microbial balance and improving survival, although it did not show superiority to vancomycin. These findings suggest that thioridazine has potential as a novel therapeutic for CDI, either as an adjunct to existing antibiotics or as part of a combination therapy to combat antibiotic resistance. Further research, including replication studies and dose optimization, is needed to fully evaluate thioridazine's therapeutic potential.

Microbial Technologies Enhanced by Artificial Intelligence for Healthcare Applications

The combination of artificial intelligence (AI) with microbial technology marks the start of a major transformation, improving applications throughout biotechnology, especially in healthcare. With the capability of AI to process vast amounts of biological big data, advanced microbial technology allows for a comprehensive understanding of complex biological systems, advancing disease diagnosis, treatment and the development of microbial therapeutics. This mini review explores the impact of AI-integrated microbial technologies in healthcare, highlighting advancements in microbial biomarker-based diagnosis, the development of microbial therapeutics and the microbial production of therapeutic compounds. This exploration promises significant improvements in the design and implementation of health-related solutions, steering a new era in biotechnological applications.

Food additives and their impact on human health

Increasing evidence suggests that high consumption of ultra-processed foods (UPF) is associated with an increase in noncommunicable diseases, overweight, and obesity. This review aimed to verify the association of UPF with inflammatory diseases, especially allergic diseases. To identify relevant articles, an extensive literature search was conducted using the two most important search sites - PubMed and Google Scholar. Specific Medical Subject Headings (MeSHes) such as "food additives and health," "food additives and immune system," and "food additives and diseases" were used to conduct an advanced search. Emulsifiers have been, particularly, implicated in disrupting intestinal barrier function, modifying gut microbiota, and promoting inflammation, which may contribute to the development of food allergies and inflammatory diseases. While food additives serve various functions in the food industry, concerns regarding their impact on health, particularly in systemic autoimmune and metabolic conditions, have been raised. Common additives have been associated with allergic reactions, intolerances, and sensitivities.

Association between nutrient intake and inflammatory bowel disease risk: Insights from NHANES data and dose-response analysis

BACKGROUND

The role of dietary and nutritional factors in inflammatory bowel disease (IBD) remains poorly understood, necessitating further investigation. This study aims to explore the association between nutrient intake and the risk of IBD.

METHODS

This cross-sectional study utilized data from the 2009-2010 NHANES cycle, focusing on individuals with complete 24-hour dietary intake records and clinically assessed IBD information. Nutrient intake was assessed through dietary recalls and supplement data. Associations between nutrient intake and IBD risk were analyzed by propensity score matching (PSM) with balanced baseline characteristics and logistic regression. Dose-response relationships were examined by restricted cubic splines (RCS). Statistical significance was set at P < 0.05, and analyses were conducted using R software.

RESULTS

The study included 4,072 participants with clinically assessed IBD and complete nutrient intake data. In adjusted analyses, lower intake of vitamin B3, copper, phosphorus, selenium, sodium, and protein below the recommended dietary allowance may increase the risk of developing IBD. Similarly, reduced intake of vitamin B6, vitamin E, and total PUFA is associated with elevated susceptibility to IBD.

CONCLUSION

This study elucidates the intricate relationship between nutrient intake and the onset of IBD, underscoring the importance of maintaining a balanced diet for gastrointestinal health. These findings emphasize the significance of informed dietary choices in promoting intestinal wellness and potentially reducing the risk of IBD development.

Effect of Omeprazole on Esophageal Microbiota in Dogs Detected Using a Minimally Invasive Sampling Method

BACKGROUND

Omeprazole alters the esophageal microbiome (EM) of humans and has associated effects.

OBJECTIVES

To assess the changes and subsequent recovery of the EM in awake dogs after omeprazole treatment, using the esophageal string test (EST).

ANIMALS

Ten healthy, client-owned adult dogs.

METHODS

A prospective longitudinal design was employed, where esophageal samples were initially collected using EST (day 0), involving the oral administration of an EST capsule and subsequent retrieval after 15 min for pH-based segment identification. The dogs were then administered 1 mg/kg of omeprazole orally, twice daily for 14 days. Follow-up EST samplings were conducted on days 15 and 45. Samples were sequenced targeting the V3-V4 region of the 16S rRNA gene and diversity analysis along with differential sequencing (DEseq2) was performed.

RESULTS

All dogs tolerated the EST without adverse effects. The EST retrieved sufficient biofluid to characterize the EM in this group of dogs. Diversity analysis revealed no significant alterations in alpha (Observed species, Shannon and Simpson indices) and beta diversity (Bray-Curtis) across the time points after omeprazole administration.

CONCLUSIONS AND CLINICAL IMPORTANCE

Omeprazole therapy did not alter the EM of healthy dogs in this study. The application of EST in dogs illustrates its use as a minimally invasive tool for investigating the role of EM in esophageal health and disease in dogs.

m6A RNA methylation: a pivotal regulator of tumor immunity and a promising target for cancer immunotherapy

M6A modification is one of the most common regulatory mechanisms of gene expression in eukaryotic cells, influencing processes such as RNA splicing, degradation, stability, and protein translation. Studies have shown that m6A methylation is closely associated with tumorigenesis and progression, and it plays a key regulatory role in tumor immune responses. m6A modification participates in regulating the differentiation and maturation of immune cells, as well as related anti-tumor immune responses. In the tumor microenvironment, m6A modification can also affect immune cell recruitment, activation, and polarization, thereby promoting or inhibiting tumor cell proliferation and metastasis, and reshaping the tumor immune microenvironment. In recent years, immunotherapies for tumors, such as immune checkpoint inhibitors and adoptive cell immunotherapy, have been increasingly applied in clinical settings, achieving favorable outcomes. Targeting m6A modifications to modulate the immune system, such as using small-molecule inhibitors to target dysregulated m6A regulatory factors or inducing immune cell reprogramming, can enhance anti-tumor immune responses and strengthen immune cell recognition and cytotoxicity against tumor cells. m6A modification represents a new direction in tumor immunotherapy with promising clinical potential. This review discusses the regulatory role of m6A methylation on immune cells and tumor immune responses and explores new strategies for immunotherapy.

Immuno- and gut microbiota-modulatory activities of β-1,6-glucans from Lentinus edodes

The β-1,6-glucans from Lentinus edodes have a variety of biological activities. However, the research on extraction and separation of β-1,6-glucans from L. edodes is limited and the yield is low. In the present study, we obtained the high-yield and -purity β-1,6-glucans (ALEPA) from L. edodes by using a sequential extraction and separation process, which is simple and suitable for industrialization. ALEPA significantly promoted the proliferation of splenic T lymphocytes and enhanced the phagocytosis activity of peritoneal macrophages in vivo. 16S rRNA sequencing results showed that ALEPA significantly increased the α diversity of gut microbiota and upregulated the relative abundances of short chain fatty acids (SCFAs)-producing bacterial species. Consistently, the SCFAs in the cecum of mice were upregulated. On a mechanical level, we found that the immunomodulatory effect of ALEPA depended on gut microbiota. Collectively, ALEPA is a promising functional food ingredient that regulates gut microbiota and enhances immune function.

Exploring the CDCA-Scd1 Axis: Molecular Mechanisms Linking the Colitis Microbiome to Neurological Deficits

Inflammatory bowel disease is a risk factor for brain dysfunction; however, the underlying mechanisms remain largely unknown. In this study, we aimed to explore the potential molecular mechanisms through which intestinal inflammation affects brain function and to verify these mechanisms. Mice were treated with multiple cycles of 1% w/v dextran sulfate sodium (DSS) in drinking water to establish a chronic colitis model. Behavioral tests were conducted using the open field test (OFT), tail suspension test (TST), forced swimming test (FST), and Morris water maze test (MWM). Brain metabolomics, transcriptomics, and proteomics analyses were performed, and key target proteins were verified using qPCR and immunofluorescence. Four cycles of DSS administration induced colitis, anxiety, depression, and spatial memory impairment. The integrated multi-omics characterization of colitis revealed decreased brain chenodeoxycholic acid (CDCA) levels as well as reduced stearoyl-CoA desaturase (Scd1) gene and protein expression. Transplantation of the colitis microbiome resulted in anxiety, depression, impaired spatial memory, reduced CDCA content, decreased Scd1 gene and protein expression, and lower concentrations of monounsaturated fatty acids (MUFAs), palmitoleate (C16:1), and oleate (C18:1) in the brain. In addition, CDCA supplementation improved DSS-induced colitis, alleviated depression and spatial memory impairment, and increased Scd1 gene and protein expression as well as MUFA levels in the brain. The gut microbiome induced by colitis contributes to neurological dysfunction, possibly through the CDCA-Scd1 signaling axis. CDCA supplementation alleviates colitis and depressive behavior, likely by increasing Scd1 expression in the brain.

Crosstalk between gut microbiotas and fatty acid metabolism in colorectal cancer

Colorectal cancer (CRC) is the third most common malignancy globally and the second leading cause of cancer-related mortality. Its development is a multifactorial and multistage process influenced by a dynamic interplay between gut microbiota, environmental factors, and fatty acid metabolism. Dysbiosis of intestinal microbiota and abnormalities in microbiota-associated metabolites have been implicated in colorectal carcinogenesis, highlighting the pivotal role of microbial and metabolic interactions. Fatty acid metabolism serves as a critical nexus linking dietary patterns with gut microbial activity, significantly impacting intestinal health. In CRC patients, reduced levels of short-chain fatty acids (SCFAs) and SCFA-producing bacteria have been consistently observed. Supplementation with SCFA-producing probiotics has demonstrated tumor-suppressive effects, while therapeutic strategies aimed at modulating SCFA levels have shown potential in enhancing the efficacy of radiation therapy and immunotherapy in both preclinical and clinical settings. This review explores the intricate relationship between gut microbiota, fatty acid metabolism, and CRC, offering insights into the underlying mechanisms and their potential translational applications. Understanding this interplay could pave the way for novel diagnostic, therapeutic, and preventive strategies in the management of CRC.

Tryptophan metabolites profile predict remission with dietary therapy in pediatric Crohn's disease

Background

Crohn's disease (CD) exclusion diet combined with partial enteral nutrition (CDED + PEN) or exclusive enteral nutrition (EEN) is effective in inducing remission in mild-to-moderate pediatric CD. Although CDED + PEN is better tolerated and has higher compliance compared to EEN, a subset of patients does not achieve remission. Diet-induced remission is shown to be positively associated with specific changes in tryptophan-metabolites.

Objectives

To investigate whether the abundance of baseline fecal tryptophan-metabolites predicts dietary therapy outcomes in pediatric CD.

Design

Diagnostic accuracy study and secondary analysis of previously conducted Randomized Controlled Trial (RCT).

Methods

Twenty-six patients from previously performed RCT of mild-to-moderate pediatric CD were included. The patients were classified as having clinical remission (R) (n = 19 in total; CDED + PEN = 10 and to EEN = 9) or No-Remission (NR) (n = 7 in total; CDED + PEN = 3 and EEN = 4) following 6 weeks of therapy, based on the Pediatric Crohn's Disease Activity Index score (⩽10 = remission). We performed a targeted quantitative analysis of 21 tryptophan-metabolites in baseline (t = 0) fecal samples from both groups, utilizing liquid chromatography coupled with quadrupole mass spectrometry. Receiver operator characteristic curve (ROC) and random forest analysis (RFA) were used to assess the predictive power of fecal tryptophan-metabolites for dietary outcomes at baseline. Ratios of tryptophan-metabolites were compared to investigate different downstream tryptophan pathways.

Results

Baseline fecal kynurenine level was significantly higher in NR compared to R for CDED + PEN (p = 0.02) and EEN (p = 0.04). ROC analysis highlighted the robust predictive power of kynurenine for CDED + PEN (area under the curve (AUC = 0.97)) and EEN (AUC = 0.88)-induced remission. RFA corroborated these observations. The ratio serotonin/kynurenine was the strongest predictor of CDED + PEN-induced remission (AUC = 1). The ratio 5-hydroxytryptophan/kynurenine (AUC = 0.88) predicted EEN-induced remission. By combining data from CDED + PEN and EEN, kynurenine (AUC = 0.91) and ratios of quinolinic acid/kynurenine (AUC = 0.93) and kynurenine/indole-3-acetic acid (AUC = 0.88) demonstrated strong predictive performance for dietary therapy-induced remission.

Conclusion

Baseline tryptophan metabolites have the potential to serve as a biomarker for dietary remission in pediatric CD. Some tryptophan metabolite ratios showed the most promising predictive capabilities. If confirmed in validation studies, baseline fecal tryptophan markers may be able to provide much-needed guidance to personalize dietary intervention within the management of pediatric CD.

Trial registration

NCT01728870.

Nasal Microbiota Profiling as a Predictive Secondary Tool for COVID-19 Diagnosis: The Critical Role of Taxonomic Resolution

The SARS-CoV-2 pandemic has led to an urgent need for effective and rapid diagnostic tools. In the present study, we have evaluated the predictive diagnostic potential of nasal microbiota by analyzing microbial community structures at different taxonomic level resolutions-species, genus, family, order, class and phylum-using Random Forest modelling. A total of 179 nasal swabs from COVID-19-positive (n = 85) and COVID-19-negative (n = 94) individuals were sequenced using a full-length 16S rRNA sequencing (Oxford Nanopore) approach. During each iteration of the Random Forest model, the dataset was randomly split into a training set (70%) and a testing set (30%). Model performance improved with finer taxonomic resolution, achieving the highest accuracy at the Species level (AUROC = 0.821 ± 0.059) and a sensitivity of 55.6% at a specificity threshold of 90%. A progressive decline in AUROC and sensitivity was observed at broader taxonomic levels. Furthermore, Beta diversity analysis supported that microbial community structures are more distinct between COVID-19-positive and COVID-19-negative groups at finer taxonomic levels. These findings highlight the potential role of nasal microbiota profiling as a secondary diagnostic tool for COVID-19, particularly at species- and genus-level classification, and underscore the importance of high taxonomic resolution in microbiome-based diagnostics. However, limited by an uneven sample distribution and the lack of medical evaluations, further large-scale studies are needed before the nasal microbiota can be implemented in the clinical diagnostics of COVID-19.

The m6A revolution: transforming tumor immunity and enhancing immunotherapy outcomes

N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, plays a critical role in the development and progression of various diseases, including cancer, through its regulation of RNA degradation, stabilization, splicing, and cap-independent translation. Emerging evidence underscores the significant role of m6A modifications in both pro-tumorigenic and anti-tumorigenic immune responses. In this review, we provide a comprehensive overview of m6A modifications and examine the relationship between m6A regulators and cancer immune responses. Additionally, we summarize recent advances in understanding how m6A modifications influence tumor immune responses by directly modulating immune cells (e.g., dendritic cells, tumor-associated macrophages, and T cells) and indirectly affecting cancer cells via mechanisms such as cytokine and chemokine regulation, modulation of cell surface molecules, and metabolic reprogramming. Furthermore, we explore the potential synergistic effects of targeting m6A regulators in combination with immune checkpoint inhibitor (ICI) therapies. Together, this review consolidates current knowledge on the role of m6A-mediated regulation in tumor immunity, offering insights into how a deeper understanding of these modifications may identify patients who are most likely to benefit from immunotherapies.