Gut microbiota alterations are distinct for primary colorectal cancer and hepatocellular carcinoma

Recent developments in immunotherapy for gastrointestinal tract cancers

The past few decades have witnessed the rise of immunotherapy for Gastrointestinal (GI) tract cancers. The role of immune checkpoint inhibitors (ICIs), particularly programmed death protein 1 (PD-1) and PD ligand-1 antibodies, has become increasingly pivotal in the treatment of advanced and perioperative GI tract cancers. Currently, anti-PD-1 plus chemotherapy is considered as first-line regimen for unselected advanced gastric/gastroesophageal junction adenocarcinoma (G/GEJC), mismatch repair deficient (dMMR)/microsatellite instability-high (MSI-H) colorectal cancer (CRC), and advanced esophageal cancer (EC). In addition, the encouraging performance of claudin18.2-redirected chimeric antigen receptor T-cell (CAR-T) therapy in later-line GI tract cancers brings new hope for cell therapy in solid tumour treatment. Nevertheless, immunotherapy for GI tumour remains yet precise, and researchers are dedicated to further maximising and optimising the efficacy. This review summarises the important research, latest progress, and future directions of immunotherapy for GI tract cancers including EC, G/GEJC, and CRC.

A microfluidic co-culture model for investigating colonocytes-microbiota interactions in colorectal cancer

Changes in the abundance of certain bacterial species within the colorectal microbiota correlate with colorectal cancer (CRC) development. While carcinogenic mechanisms of single pathogenic bacteria have been characterized in vitro, limited tools are available to investigate interactions between pathogenic bacteria and both commensal microbiota and colonocytes in a physiologically relevant tumor microenvironment. To address this, we developed a microfluidic device that can be used to co-culture colonocyte spheroids and colorectal microbiota. The device was used to explore the effect of Fusobacterium nucleatum, an opportunistic pathogen associated with colorectal cancer development in humans, on colonocyte gene expression and microbiota composition. F. nucleatum altered the transcription of genes involved in cytokine production, epithelial-to-mesenchymal transition, and proliferation in colonocytes in a contact-independent manner; however, most of these effects were significantly diminished by the presence of commensal microbiota. Interestingly, F. nucleatum significantly altered the abundance of multiple bacterial clades associated with mucosal immune responses and cancer development in the colon. Our results highlight the importance of evaluating the potential carcinogenic activity of pathogens in the context of a commensal microbiota, and the potential to discover novel inter-species microbial interactions in the CRC microenvironment.

N6-methyladenosine-dependent signaling in colorectal cancer: Functions and clinical potential

Colorectal cancer (CRC) ranks as the third most prevalent malignancy worldwide. Despite the gradual expansion of therapeutic options for CRC, its clinical management remains a formidable challenge. And, because of the current dearth of technical means for early CRC screening, most patients are diagnosed at an advanced stage. Therefore, it is imperative to develop novel diagnostic and therapeutic tools for this disease. N6-methyladenosine (m6A), the predominant RNA modification in eukaryotes, can be recognized by m6A-specific methylated reading proteins to modulate gene expression. Studies have revealed that CRC disrupts m6A homeostasis through various mechanisms, thereby sustaining aberrant signal transduction and promoting its own progression. Consequently, m6A-based diagnostic and therapeutic strategies have garnered widespread attention. Although utilizing m6A as a biomarker and drug target has demonstrated promising feasibility, existing observations primarily stem from preclinical models; henceforth necessitating further investigation and resolution of numerous outstanding issues.

Exopolysaccharides Produced by Bifidobacterium longum subsp. longum YS108R Ameliorates DSS-Induced Ulcerative Colitis in Mice by Improving the Gut Barrier and Regulating the Gut Microbiota

Ulcerative colitis (UC) is a major disease that has endangered human health. Our previous study demonstrated that Bifidobacterium longum subsp. longum YS108R, a ropy exopolysaccharide (EPS)-producing bacterium, could alleviate UC in mice, but it is unclear whether EPS is the key substance responsible for its action. In this study, we proposed to investigate the remitting effect of EPS from B. longum subsp. longum YS108R on UC in a DSS-induced UC mouse model. Water extraction and alcohol precipitation were applied to extract EPS from the supernatant of B. longum subsp. longum YS108R culture. Then the animal trial was performed, and the results indicated that YS108R EPS ameliorated colonic pathological damage and the intestinal barrier. YS108R EPS suppressed inflammation via NF-κB signaling pathway inhibition and attenuated oxidative stress via the Nrf2 signaling pathway activation. Remarkably, YS108R EPS regulated gut microbiota, as evidenced by an increase in short-chain fatty acid (SCFA)-producing bacteria and a decline in Gram-negative bacteria, resulting in an increase of propionate and butyrate and a reduction of lipopolysaccharide (LPS). Collectively, YS108R EPS manipulated the intestinal microbiota and its metabolites, which further improved the intestinal barrier and inhibited inflammation and oxidative stress, thereby alleviating UC.

Microbiota in colorectal cancer related to liver metastasis

The prevalence of colorectal cancer (CRC) is increasing annually and metastasis is the principal cause of death in patients with CRC, with the liver being the most frequently affected site. Many studies have shown a strong interplay between the gut flora, particularly Fusobacterium nucleatum (F. nucleatum), Escherichia coli, and Bacteroides fragilis, and the development of gut tumors. Some strains can induce gut inflammation and produce toxins that directly harm gut epithelial cells, ultimately accelerating the onset and progression of CRC. However, little clinical evidence exists on the specific interplay between the gut microflora and colorectal cancer liver metastasis (CRLM). Some research showed the existence of viable F. nucleatum in distant metastasis of CRC. Subsequently, gut microbiota products, such as lipopolysaccharides, sodium butyrate, and protein cathepsin K, were also found to affect the development of CRC. This article summarizes the mechanism and research status of the interplay between gut microflora and CRLM, discusses the importance of gut microflora in the treatment of CRLM, and proposes a new approach to understanding the mechanism of CRLM and potential treatments for the microbiome. It is anticipated that the gut microbiota will be a formidable therapeutic and prophylactic tool for treating and preventing CRLM.

Association of blood cell-based inflammatory markers with gut microbiota and cancer incidence in the Rotterdam study

The immune response-gut microbiota interaction is implicated in various human diseases, including cancer. Identifying the link between the gut microbiota and systemic inflammatory markers and their association with cancer will be important for our understanding of cancer etiology. The current study was performed on 8090 participants from the population-based Rotterdam study. We found a significant association (false discovery rate [FDR] ≤0.05) between lymphocytes and three gut microbial taxa, namely the family Streptococcaceae, genus Streptococcus, and order Lactobacillales. In addition, we identified 95 gut microbial taxa that were associated with inflammatory markers (p < 0.05). Analyzing the cancer data, we observed a significant association between higher systemic immune-inflammation index (SII) levels at baseline (hazard ratio (HR): 1.65 [95% confidence interval (CI); 1.10-2.46, p ≤ 0.05]) and a higher count of lymphocytes (HR: 1.38 [95% CI: 1.15-1.65, p ≤ 0.05]) and granulocytes (HR: 1.69 [95% CI: 1.40-2.03, p ≤ 0.05]) with increased risk of lung cancer after adjusting for age, sex, body mass index (BMI), and study cohort. This association was lost for SII and lymphocytes after additional adjustment for smoking (SII = HR:1.46 [95% CI: 0.96-2.22, p = 0.07] and lymphocytes = HR: 1.19 [95% CI: 0.97-1.46, p = 0.08]). In the stratified analysis, higher count of lymphocyte and granulocytes at baseline were associated with an increased risk of lung cancer in smokers after adjusting for age, sex, BMI, and study cohort (HR: 1.33 [95% CI: 1.09-1.62, p ≤0.05] and HR: 1.57 [95% CI: 1.28-1.92, p ≤0.05], respectively). Our study revealed a positive association between gut microbiota, higher SII levels, and higher lymphocyte and granulocyte counts, with an increased risk of developing lung cancer.

The colibactin-producing Escherichia coli alters the tumor microenvironment to immunosuppressive lipid overload facilitating colorectal cancer progression and chemoresistance

Intratumoral bacteria flexibly contribute to cellular and molecular tumor heterogeneity for supporting cancer recurrence through poorly understood mechanisms. Using spatial metabolomic profiling technologies and 16SrRNA sequencing, we herein report that right-sided colorectal tumors are predominantly populated with Colibactin-producing Escherichia coli (CoPEC) that are locally establishing a high-glycerophospholipid microenvironment with lowered immunogenicity. It coincided with a reduced infiltration of CD8+ T lymphocytes that produce the cytotoxic cytokines IFN-γ where invading bacteria have been geolocated. Mechanistically, the accumulation of lipid droplets in infected cancer cells relied on the production of colibactin as a measure to limit genotoxic stress to some extent. Such heightened phosphatidylcholine remodeling by the enzyme of the Land's cycle supplied CoPEC-infected cancer cells with sufficient energy for sustaining cell survival in response to chemotherapies. This accords with the lowered overall survival of colorectal patients at stage III-IV who were colonized by CoPEC when compared to patients at stage I-II. Accordingly, the sensitivity of CoPEC-infected cancer cells to chemotherapies was restored upon treatment with an acyl-CoA synthetase inhibitor. By contrast, such metabolic dysregulation leading to chemoresistance was not observed in human colon cancer cells that were infected with the mutant strain that did not produce colibactin (11G5∆ClbQ). This work revealed that CoPEC locally supports an energy trade-off lipid overload within tumors for lowering tumor immunogenicity. This may pave the way for improving chemoresistance and subsequently outcome of CRC patients who are colonized by CoPEC.

Washed microbiota transplantation improves haemoglobin levels in anaemia of chronic disease

BACKGROUND

Anaemia of chronic disease (ACD) is the second most common type of anaemia and lacks an effective treatment. Patients with anaemia are reported to have altered gut microbial profiles, which may affect erythropoiesis. Here, we investigated the gut microbial features of patients with ACD and determined whether regulating gut microbiota using washed microbiota transplantation (WMT) was effective in treating ACD.

METHODS

We compared the gut microbiota profile of patients with ACD and healthy controls, evaluated the efficacy of WMT on haematological parameters in the patients, and analysed the alterations in gut microbiota after WMT treatment.

RESULTS

Patients with ACD had lower gut microbial richness, and differences in microbial composition and function, relative to healthy controls. Additionally, the relative abundances of two butyrate-producing genera Lachnospiraceae NK4A136 group and Butyricicoccus, were positively correlated with the haemoglobin (HGB) level and lower in patients with ACD than controls. WMT significantly increased HGB levels in patients with ACD. After the first, second and third WMT rounds, normal HGB levels were restored in 27.02%, 27.78% and 36.37% (all p < .05) of patients with ACD, respectively. Moreover, WMT significantly increased the abundance of butyrate-producing genera and downregulated gut microbial functions that were upregulated in patients with ACD.

CONCLUSIONS

Patients with ACD exhibited differences in gut microbial composition and function relative to healthy controls. WMT is an effective treatment for ACD that reshapes gut microbial composition, restores butyrate-producing bacteria and regulates the functions of gut microbiota.

Effects of different processed tomatoes on carotenoid release and microbiota composition during in vitro gastrointestinal digestion and colonic fermentation

Carotenoids in tomatoes confer significant health benefits to humans but with the disadvantage of the carotenoids from raw tomatoes not being easily absorbed for utilization. Thus, this study aimed to investigate the effects of different cooking processes on carotenoid release and human gut microbiota composition during in vitro simulated gastrointestinal digestion of tomatoes. The results showed that stir-frying significantly increased the release of lycopene and β-carotene during gastrointestinal digestion, with boiling being the second most effective treatment. The boiling-treated tomatoes enhanced the carotenoid release during in vitro fermentation. Gut microbiota analysis revealed that the digestion of the raw and boiled tomatoes promoted the growth of potentially beneficial microbiota while reducing the ratio of Firmicutes/Bacteroides, which potentially helps prevent obesity. Boiling treatment significantly reduced the growth of Peptostreptococcus and was negatively correlated with carotenoid release. Overall, the boiling-treated tomatoes were more effective than the raw or stir-fried tomatoes in terms of both colon health benefits and carotenoid release.

Intestinal microbiota: A bridge between intermittent fasting and tumors

Intestinal microbiota and their metabolites are essential for maintaining intestinal health, regulating inflammatory responses, and enhancing the body's immune function. An increasing number of studies have shown that the intestinal microbiota is tightly tied to tumorigenesis and intervention effects. Intermittent fasting (IF) is a method of cyclic dietary restriction that can improve energy metabolism, prolong lifespan, and reduce the progression of various diseases, including tumors. IF can affect the energy metabolism of tumor cells, inhibit tumor cell growth, improve the function of immune cells, and promote an anti-tumor immune response. Interestingly, recent research has further revealed that the intestinal microbiota can be impacted by IF, in particular by changes in microbial composition and metabolism. These findings suggest the complexity of the IF as a promising tumor intervention strategy, which merits further study to better understand and encourage the development of clinical tumor intervention strategies. In this review, we aimed to outline the characteristics of the intestinal microbiota and its mechanisms in different tumors. Of note, we summarized the impact of IF on intestinal microbiota and discussed its potential association with tumor suppressive effects. Finally, we proposed some key scientific issues that need to be addressed and envision relevant research prospects, which might provide a theoretical basis and be helpful for the application of IF and intestinal microbiota as new strategies for clinical interventions in the future.

From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes

The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.

Effect of purple sweet potato-derived anthocyanins on heat stress response in Wenchang chickens and preliminary mechanism study

This study was conducted to investigate the beneficial effect of purple sweet potato anthocyanins (PSPA) on growth performance, oxidative status, immune response, intestinal morphology, and intestinal flora homeostasis in heat-stressed Wenchang chickens. A total of 100 Wenchang chickens (50-day-old) were randomly assigned to 5 groups, including the thermoneutral environment (TN) group (26°C); high-temperature stressed (HS) group (33°C ± 1°C); low-dose PSPA treatment (L_HS) group (8 mg/kg body weight, 33°C ± 1°C); medium-dose PSPA treatment (M_HS) group and high-dose PSPA treatment (H_HS) group (16 mg/kg and 32 mg/kg body weight, respectively, 33°C ± 1°C). The results showed that PSPA reversed the adverse effects of heat stress on growth performance, meat quality, and carcass characteristics. And the effect was associated with the concentration of PSPA partially. Heat stress increased the serum lipids of Wenchang chickens. LDL-C, TG, TC, and FFA in the serum were significantly decreased, and HDL-C and LPS in the serum were increased by PSPA treatment. The digestive enzymes in duodenal chyme were significantly (P < 0.05) increased by PSPA treatment. And PSPA treatment significantly (P < 0.05) enhanced the redox status by improving antioxidant parameters (GSH-Px and SOD) and decreasing the MDA level in the serum and liver. Moreover, the level of inflammatory cytokines was significantly (P < 0.05) regulated by PSPA treatment compared to the HS group. The villus length and goblet cell numbers after PSPA treatment were significantly higher than HS group. Furthermore, PSPA also played protection on the intestine structure by decreasing the level of D-LA and DAO. 16S rRNA sequencing revealed the microbial composition was altered by PSPA, and Acetanaerobacterium and Oscillibacter were dominant in the H_HS group. Microbial functional prediction indicated that function pathways based on KEGG and metacyc database were regulated by PSPA, and intestinal flora correlated with metabolic function significantly. The spearman correlation analysis showed that Saccharibacteria and Clostridium_IV correlated with the serum lipids, antioxidant, and inflammatory cytokines. Collectively, these findings suggest that PSPA has a positive effect against heat stress in poultry.

Maternal high-fat diet increases the susceptibility of offspring to colorectal cancer via the activation of intestinal inflammation

A high-fat diet plays a key role in the pathogenesis of colorectal cancer, and this effect on the gut can also occur in the offspring of mothers with a high-fat diet. In this review, we discuss the role of a high-fat diet in the pathogenesis of colorectal cancer and summarize the effects of a maternal high-fat diet on the activation of inflammation and development of colorectal cancer in offspring. Studies have found that a maternal high-fat diet primarily induces an inflammatory response in the colorectal tissue of both the mother herself and the offspring during pregnancy. This leads to the accumulation of inflammatory cells in the colorectal tissue and the release of inflammatory cytokines, which further activate the NF-κb and related inflammatory signaling pathways. Research suggests that high levels of lipids and inflammatory factors from mothers with a high-fat diet are passed to the offspring through the transplacental route, which induces colorectal inflammation, impairs the intestinal microecological structure and the intestinal barrier, and interferes with intestinal development in the offspring. This in turn activates the NF-κb and related signaling pathways, which further aggravates intestinal inflammation. This process of continuous inflammatory stimulation and repair may promote the uncontrolled proliferation of colorectal mucosal cells in the offspring, thus increasing their susceptibility to colorectal cancer.

FXR agonists for colorectal and liver cancers, as a stand-alone or in combination therapy

Farnesoid X receptor (FXR, NR1H4) is generally considered as a tumor suppressor of colorectal and liver cancers. The interaction between FXR, bile acids (BAs) and gut microbiota is closely associated with an increased risk of colorectal and liver cancers. Increasing evidence shows that FXR agonists may be potential therapeutic agents for colorectal and liver cancers. However, FXR agonists alone do not produce the desired results due to the complicated pathogenesis and single therapeutic mechanism, which suggests that effective treatments will require a multimodal approach. Based on the principle of improvingefficacy andreducingside effects, combination therapy is currently receiving considerable attention. In this review, colorectal and liver cancers are grouped together to discuss the effects of FXR agonists alone or in combination for combating the two cancers. We hope that this review will provide a theoretical basis for the clinical application of novel FXR agonists or combination with FXR agonists against colorectal and liver cancers.

Protective Effect of Polyphenols, Protein, Peptides, and Polysaccharides on Alcoholic Liver Disease: A Review of Research Status and Molecular Mechanisms

Alcoholic liver disease (ALD) has emerged as an important public health problem in the world. The polyphenols, protein, peptides, and polysaccharides have attracted attention for prevention or treatment of ALD. Therefore, this paper reviews the pathogenesis of ALD, the relationship between polyphenols, peptides, polysaccharides, and ALD, and expounds the mechanism of gut microbiota on protecting ALD. It is mainly found that the hydroxyl group of polyphenols endows it with antioxidation to protect ALD. The ALD protection of bioactive peptides is related to amino acid composition. The ALD protection of polysaccharides is related to the primary structure. Meanwhile, polyphenols, protein, peptides, and polysaccharides prevent or treat ALD by antioxidation, anti-inflammatory, antiapoptosis, lipid metabolism, and gut microbiota regulation. This contribution provides updated information on polyphenols, protein, peptides, and polysaccharides in response to ALD, which will not only facilitate the development of novel bioactive components but also the future application of functional food raw materials will be promoted.

Irinotecan-gut microbiota interactions and the capability of probiotics to mitigate Irinotecan-associated toxicity

BACKGROUND

Irinotecan is a chemotherapeutic agent used to treat a variety of tumors, including colorectal cancer (CRC). In the intestine, it is transformed into SN-38 by gut microbial enzymes, which is responsible for its toxicity during excretion.

OBJECTIVE

Our study highlights the impact of Irinotecan on gut microbiota composition and the role of probiotics in limiting Irinotecan-associated diarrhea and suppressing gut bacterial β-glucuronidase enzymes.

MATERIAL AND METHODS

To investigate the effect of Irinotecan on the gut microbiota composition, we applied 16S rRNA gene sequencing in three groups of stool samples from healthy individuals, colon cancer, and Irinotecan treated patients (n = 5/group). Furthermore, three Lactobacillus spp.; Lactiplantibacillus plantarum (L. plantarum), Lactobacillus acidophilus (L. acidophilus), Lacticaseibacillus rhamnosus (L. rhamnosus) were used in a single and mixed form to in-vitro explore the effect of probiotics on the expression of β-glucuronidase gene from E. coli. Also, probiotics were introduced in single and mixed forms in groups of mice before the administration of Irinotecan, and their protective effects were explored by assessing the level of reactive oxidative species (ROS) as well as studying the concomitant intestinal inflammation and apoptosis.

RESULTS

The gut microbiota was disturbed in individuals with colon cancer and after Irinotecan treatment. In the healthy group, Firmicutes were more abundant than Bacteriodetes, which was the opposite in the case of colon-cancer or Irinotecan treated groups. Actinobacteria and Verrucomicrobia were markedly present within the healthy group, while Cyanobacteria were noted in colon-cancer and the Irinotecan-treated groups. Enterobacteriaceae and genus Dialister were more abundant in the colon-cancer group than in other groups. The abundance of Veillonella, Clostridium, Butryicicoccus, and Prevotella were increased in Irinotecan-treated groups compared to other groups. Using Lactobacillus spp. mixture in mice models significantly relieved Irinotecan-induced diarrhea through the reduction of both β-glucuronidase expression and ROS, in addition to guarding gut epithelium against microbial dysbiosis and proliferative crypt injury.

CONCLUSIONS

Irinotecan-based chemotherapy altered intestinal microbiota. The gut microbiota participates greatly in determining both the efficacy and toxicity of chemotherapies, of which the toxicity of Irinotecan is caused by the bacterial ß-glucuronidase enzymes. The gut microbiota can now be aimed and modulated to promote efficacy and decrease the toxicity of chemotherapeutics. The used probiotic regimen in this study lowered mucositis, oxidative stress, cellular inflammation, and apoptotic cascade induction of Irinotecan.

Alterations in gut microbiota and urine metabolomics in infants with yin-deficiency constitution aged 0–2 years

Background

Based on the constitution theroy, infants are classified into balanced constitution (BC) and unbalanced constitution. Yin-deficiency constitution (YINDC) is a common type of unbalanced constitutions in Chinese infants. An infant's gut microbiota directly affects the child's health and has long-term effects on the maturation of the immune and endocrine systems throughout life. However, the gut microbiota of infants with YINDC remains unknown. Herein, we aimed to evaluate the intestinal flora profiles and urinary metabolites in infant with YINDC, find biomarkers to identify YINDC, and promote our understanding of infant constitution classification.

Methods

Constitutional Medicine Questionnaires were used to assess the infants' constitution types. 47 infants with 21 cases of YINDC and 26 cases of BC were included, and a cross-sectional sampling of stool and urine was conducted. Fecal microbiota was characterized using 16S rRNA sequencing, and urinary metabolomics was profiled using UPLC-Q-TOF/MS method. YINDC markers with high accuracy were identified using receiver operating characteristic (ROC) analysis.

Results

The diversity and composition of intestinal flora and urinary metabolites differed significantly between the YINDC and BC groups. A total of 13 obviously different genera and 55 altered metabolites were identified. Stool microbiome shifts were associated with urine metabolite changes. A combined marker comprising two genera may have a high potential to identify YINDC with an AUC of 0.845.

Conclusions

Infants with YINDC had a unique gut microbiota and metabolomic profile resulting in a constitutional microclassification. The altered gut microbiome in YINDC may account for the higher risk of cardiovascular diseases. Metabolomic analysis of urine showed that metabolic pathways, including histidine metabolism, proximal tubule bicarbonate reclamation, arginine biosynthesis, and steroid hormone biosynthesis, were altered in infants with YINDC. Additionally, the combined bacterial biomarker had the ability to identify YINDC. Identifying YINDC in infancy and intervening at an early stage is crucial for preventing cardiovascular diseases.

Biomarker discovery and application-An opportunity to resolve the challenge of liver cancer diagnosis and treatment

Liver cancer is one of the most common malignancies, with severe morbidity and mortality. While considerable progress has been made in liver cancer treatment, the 5-year overall survival (OS) of patients has not improved significantly. Reasons include the inadequate capability of early screening and diagnosis, a high incidence of recurrence and metastasis, a high degree of tumor heterogeneity, and an immunosuppressive tumor microenvironment. Therefore, the identification and validation of specific and robust liver cancer biomarkers are of major importance for early screening, timely diagnosis, accurate prognosis, and the prevention of tumor progression. In this review, we highlight some of the latest research progress and potential applications of liver cancer biomarkers, describing hotspots and prospective directions in biomarker discovery.

Gut microbiota and colorectal cancer metastasis

Gut microbiota play critical roles in the development of colorectal cancer (CRC) metastasis, but the underlying mechanisms remain elusive. This review discusses the molecular mechanisms by which the gut microbiota contribute to a tumor-permissive microenvironment and facilitate malignant transformation and dissemination of tumor cells, thereby mediating CRC metastasis.

Frizzled 7 modulates goblet and Paneth cell fate, and maintains homeostasis in mouse intestine

Intestinal homeostasis depends on interactions between the intestinal epithelium, the immune system and the microbiota. Because of these complicated connections, there are many problems that need to be solved. Current research has indicated that genes targeted by Wnt signaling are responsible for controlling intestinal stem cell fate and for modulating intestinal homeostasis. Our data show that loss of frizzled 7 (Fzd7), an important element in Wnt signaling, interrupts the differentiation of mouse intestinal stem cells into absorptive progenitors instead of secretory progenitors (precursors of goblet and Paneth cells). The alteration in canonical Wnt and Notch signaling pathways interrupts epithelial homeostasis, resulting in a decrease in physical protection in the intestine. Several phenotypes in our Fzd7-deleted model were similar to the features of enterocolitis, such as shortened intestines, decreased numbers of goblet cells and Paneth cells, and severe inflammation. Additionally, loss of Fzd7 exacerbated the defects in a chemical-induced colitis model and could initiate tumorigenesis. These findings may provide important information for the discovery of efficient therapeutic methods to treat enterocolitis and related cancers in the intestines.

Altered Gut Microbiota Composition and Its Potential Association in Patients with Advanced Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is the second-most-common cause of cancer death. In recent years, studies have suggested that intestinal microbiota dysregulation is closely related to HCC and can affect the therapeutic efficacy of immune checkpoint inhibitors. However, there are few data on the relationship between altered gut microbiota composition and its potential association in patients with advanced hepatocellular carcinoma. Hence, in this study, we aimed to investigate the gut microbiota profile associated with advanced hepatocarcinoma. In total, 20 patients with advanced hepatocarcinoma and 20 matched healthy participants were recruited. Stool samples were collected for 16S rRNA sequencing to confirm intestinal microbiota dysbiosis. The results showed that the Nseqs index in advanced hepatocarcinoma patients was significantly different compared with that in healthy individuals, while the butyrate-producing bacteria decreased and LPS-producing bacteria increased. Meanwhile, Lactobacillus, Anaerostipes, Fusicatenibacter, Bifidobacterium, and Faecalibacterium were significantly correlated with AFP, ALT, AST, and PIVKA. Our findings characterized the gut microbiota composition of advanced hepatocarcinoma, providing an experimental basis and theoretical support for using microbiota to regulate immunotherapy, achieve potential biomarkers for diagnosis, and improve the effect of clinical treatment for patients with advanced hepatocarcinoma.

Investigation of the gut microbiome, bile acid composition and host immunoinflammatory response in a model of azoxymethane-induced colon cancer at discrete timepoints

BACKGROUND

Distinct sets of microbes contribute to colorectal cancer (CRC) initiation and progression. Some occur due to the evolving intestinal environment but may not contribute to disease. In contrast, others may play an important role at particular times during the tumorigenic process. Here, we describe changes in the microbiota and host over the course of azoxymethane (AOM)-induced tumorigenesis.

METHODS

Mice were administered AOM or PBS and were euthanised 8, 12, 24 and 48 weeks later. Samples were analysed using 16S rRNA gene sequencing, UPLC-MS and qRT-PCR.

RESULTS

The microbiota and bile acid profile showed distinct changes at each timepoint. The inflammatory response became apparent at weeks 12 and 24. Moreover, significant correlations between individual taxa, cytokines and bile acids were detected. One co-abundance group (CAG) differed significantly between PBS- and AOM-treated mice at week 24. Correlation analysis also revealed significant associations between CAGs, bile acids and the bile acid transporter, ASBT. Aberrant crypt foci and adenomas were first detectable at weeks 24 and 48, respectively.

CONCLUSION

The observed changes precede host hyperplastic transformation and may represent early therapeutic targets for the prevention or management of CRC at specific timepoints in the tumorigenic process.

Oral Microbiota as Novel Biomarkers for Colorectal Cancer Screening

Alterations of the gut microbiome in cases of colorectal cancer (CRC) hint at the involvement of host-microbe interactions in the onset and progression of CRC and also, possibly, provide novel ways to detect and prevent CRC early. The aim of the present study was to evaluate whether the oral and fecal microbiomes of an individual can be suitable for CRC screening. Oral and fecal samples (n = 80) were gathered in Taleghani hospital, affiliated with Shahid Beheshti University of Medical Sciences, Tehran-Iran, from CRC stage 0 and I patients and healthy controls (HCs), who were screened for the first time. Microbial metagenomics assays were performed for studying microbiota profiles in all oral and fecal samples gathered. An abundance of top bacterial genera from both types of specimens (fecal and saliva samples) revealed a distinction between CRC patients and HCs. In saliva samples, the α diversity index was different between the microbiome of HCs and CRC patients, while β diversity showed a densely clustered microbiome in the HCs but a more dispersed pattern in CRC cases. The α and β diversity of fecal microbiota between HCs and CRC patients showed no statistically significant differences. Bifidobacterium was identified as a potential bacterial biomarker in CRC saliva samples, while Fusobacterium, Dialister, Catonella, Tennerella, Eubacterium-brachy-group, and Fretibacterium were ideal to distinguish HCs from CRC patients. One of the reasons for the heterogeneity of CRC may be the gastrointestinal (GI) tract microbiota, which can also cause systematic resistance to CRC. Moreover, an evaluation of saliva microbiota might offer a suitable screening test for the early detection of this malignancy, providing more accurate results than its fecal counterpart.

Dysbiosis: The first hit for digestive system cancer

Gastrointestinal cancer may be associated with dysbiosis, which is characterized by an alteration of the gut microbiota. Understanding the role of gut microbiota in the development of gastrointestinal cancer is useful for cancer prevention and gut microbiota-based therapy. However, the potential role of dysbiosis in the onset of tumorigenesis is not fully understood. While accumulating evidence has demonstrated the presence of dysbiosis in the intestinal microbiota of both healthy individuals and patients with various digestive system diseases, severe dysbiosis is often present in patients with digestive system cancer. Importantly, specific bacteria have been isolated from the fecal samples of these patients. Thus, the association between dysbiosis and the development of digestive system cancer cannot be ignored. A new model describing this relationship must be established. In this review, we postulate that dysbiosis serves as the first hit for the development of digestive system cancer. Dysbiosis-induced alterations, including inflammation, aberrant immune response, bacteria-produced genotoxins, and cellular stress response associated with genetic, epigenetic, and/or neoplastic changes, are second hits that speed carcinogenesis. This review explains the mechanisms for these four pathways and discusses gut microbiota-based therapies. The content included in this review will shed light on gut microbiota-based strategies for cancer prevention and therapy.

Interactions between Dietary Micronutrients, Composition of the Microbiome and Efficacy of Immunotherapy in Cancer Patients

The effectiveness of immunotherapy in cancer patients depends on the activity of the host's immune system. The intestinal microbiome is a proven immune system modulator, which plays an important role in the development of many cancers and may affect the effectiveness of anti-cancer therapy. The richness of certain bacteria in the gut microbiome (e.g., Bifidobacterium spp., Akkermanisa muciniphila and Enterococcus hire) improves anti-tumor specific immunity and the response to anti-PD-1 or anti-PD-L1 immunotherapy by activating antigen-presenting cells and cytotoxic T cells within the tumor. Moreover, micronutrients affect directly the activities of the immune system or regulate their function by influencing the composition of the microbiome. Therefore, micronutrients can significantly influence the effectiveness of immunotherapy and the development of immunorelated adverse events. In this review, we describe the relationship between the supply of microelements and the abundance of various bacteria in the intestinal microbiome and the effectiveness of immunotherapy in cancer patients. We also point to the function of the immune system in the case of shifts in the composition of the microbiome and disturbances in the supply of microelements. This may in the future become a therapeutic target supporting the effects of immunotherapy in cancer patients.

Combining p-values from various statistical methods for microbiome data

MOTIVATION

In the field of microbiome analysis, there exist various statistical methods that have been developed for identifying differentially expressed features, that account for the overdispersion and the high sparsity of microbiome data. However, due to the differences in statistical models or test formulations, it is quite often to have inconsistent significance results across statistical methods, that makes it difficult to determine the importance of microbiome taxa. Thus, it is practically important to have the integration of the result from all statistical methods to determine the importance of microbiome taxa. A standard meta-analysis is a powerful tool for integrative analysis and it provides a summary measure by combining p-values from various statistical methods. While there are many meta-analyses available, it is not easy to choose the best meta-analysis that is the most suitable for microbiome data.

RESULTS

In this study, we investigated which meta-analysis method most adequately represents the importance of microbiome taxa. We considered Fisher's method, minimum value of p method, Simes method, Stouffer's method, Kost method, and Cauchy combination test. Through simulation studies, we showed that Cauchy combination test provides the best combined value of p in the sense that it performed the best among the examined methods while controlling the type 1 error rates. Furthermore, it produced high rank similarity with the true ranks. Through the real data application of colorectal cancer microbiome data, we demonstrated that the most highly ranked microbiome taxa by Cauchy combination test have been reported to be associated with colorectal cancer.

Gut Microbiota Host-Gene Interaction

Studies carried out in the last ten years have shown that the metabolites made up from the gut microbiota are essential for multiple functions, such as the correct development of the immune system of newborns, interception of pathogens, and nutritional enrichment of the diet. Therefore, it is not surprising that alteration of the gut microbiota is the starting point of gastrointestinal infection, obesity, type 2 diabetes, inflammatory bowel disease, colorectal cancer, and lung cancer. Diet changes and antibiotics are the major factors damaging the gut microbiota. Early exposure of the newborns to antibiotics may prevent their correct development of the immune system, exposing them to pathogen infections, allergies, and chronic inflammatory diseases. We already know much on how host genes, microbiota, and the environment interact, owing to experiments in several model animals, especially in mice; advances in molecular technology; microbiota transplantation; and comparative metagenomic analysis. However, much more remains to be known. Longitudinal studies on patients undergoing to therapy, along with the identification of bacteria prevalent in responding patients may provide valuable data for improving therapies.

Dietary Polyphenols Alleviate Autoimmune Liver Disease by Mediating the Intestinal Microenvironment: Challenges and Hopes

Autoimmune liver disease is a chronic liver disease caused by an overactive immune response in the liver that imposes a significant health and economic cost on society. Due to the side effects of existing medicinal medications, there is a trend toward seeking natural bioactive compounds as dietary supplements. Currently, dietary polyphenols have been proven to have the ability to mediate gut-liver immunity and control autoimmune liver disease through modulating the intestinal microenvironment. Based on the preceding, this Review covers the many forms of autoimmune liver illnesses, their pathophysiology, and the modulatory effects of polyphenols on immune disorders. Finally, we focus on how polyphenols interact with the intestinal milieu to improve autoimmune liver disease. In conclusion, we suggest that dietary polyphenols have the potential as gut-targeted modulators for the prevention and treatment of autoimmune liver disease and highlight new perspectives and critical issues for future pharmacological applications.

Chinese herbal medicine anticancer cocktail soup activates immune cells to kill colon cancer cells by regulating the gut microbiota-Th17 axis

Chinese herbal medicines are effective for treating colon cancer (CC). CC development is reportedly associated with gut microbiota dysbiosis and immune function dysregulation. Herein we explored the therapeutic effects of a Chinese herbal medicine anticancer cocktail soup (CHMACS) on mice with CC and also explored its regulatory effects on gut microbiota. In vivo experiments indicated that CHMACS significantly inhibited the proliferation and tumorigenicity of CC cells. Further, CHMACS treatment decreased the proportion of CD8⁺ T, natural killer, and Th17 cells. HPLC/MS analysis showed that CHMACS comprised 227 active components. 16S rRNA sequencing revealed, for example, an increase in the relative abundance of uncultured_bacterium_g_Turicibacter and a decrease in that of uncultured_bacterium_g_Coriobacteriaceae_UCG-002 in gut microbiota of CHMACS-treated mice. Microbial diversity cluster analysis revealed that Verrucomicrobia, Spirochaetes, Fusobacteria, Patescibacteria, and Firmicutes contributed the most to fecal microbial diversity. Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis and clusters of orthologous groups of protein annotation indicated that CHMACS treatment induced amino acid metabolism and suppressed carbohydrate metabolism. Moreover, we found a strong association between changes in metabolites and immune cell maturation and activation. To summarize, our findings suggest that CHMACS kills CC cells by regulating gut microbiota and activating immune cells.

Effect of Bifidobacterium animalis subsp. lactis SF on enhancing the tumor suppression of irinotecan by regulating the intestinal flora

The gut microbiota plays a role in tumor therapy by participating in immune regulation. Here, we demonstrated through 8-day probiotic supplementation experiments and fecal microbiota transplantation experiments that Bifidobacterium animalis subsp. lactis SF enhanced the antitumor effect of irinotecan and prevented the occurrence of intestinal damage by modulating the gut microbiota and reducing the relative abundance of pro-inflammatory microbiota. Therefore, the intestinal inflammation was inhibited, the TGF-β leakage was reduced, and the PI3K/AKT pathway activation was inhibited. Thus, the tumor apoptotic autophagy was finally promoted. Simultaneously, the reduction of TGF-β relieved the immunosuppression caused by CPT-11, promoted the differentiation of CD4⁺ and CD8⁺ T cells in tumor tissue, and consequently inhibited tumor growth and invasion. This study disclosed the mechanism of B. lactis SF assisting CPT-11 in antitumor activity and suggested that B. lactis SF plays a new role in anticancer effects as a nutritional intervention.

Obese Individuals With and Without Phlegm-Dampness Constitution Show Different Gut Microbial Composition Associated With Risk of Metabolic Disorders

Background

Obesity is conventionally considered a risk factor for multiple metabolic diseases, such as dyslipidemia, type 2 diabetes, hypertension, and cardiovascular disease (CVD). However, not every obese patient will progress to metabolic disease. Phlegm-dampness constitution (PDC), one of the nine TCM constitutions, is considered a high-risk factor for obesity and its complications. Alterations in the gut microbiota have been shown to drive the development and progression of obesity and metabolic disease, however, key microbial changes in obese patients with PDC have a higher risk for metabolic disorders remain elusive.

Methods

We carried out fecal 16S rRNA gene sequencing in the present study, including 30 obese subjects with PDC (PDC), 30 individuals without PDC (non-PDC), and 30 healthy controls with balanced constitution (BC). Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.

Results

Obese individuals with PDC had higher BMI, waist circumference, hip circumference, and altered composition of their gut microbiota compared to non-PDC obese individuals. At the phylum level, the gut microbiota was characterized by increased abundance of Bacteroidetes and decreased levels of Firmicutes and Firmicutes/Bacteroidetes ratio. At the genus level, Faecalibacterium, producing short-chain fatty acid, achieving anti-inflammatory effects and strengthening intestinal barrier functions, was depleted in the PDC group, instead, Prevotella was enriched. Most PDC-associated bacteria had a stronger correlation with clinical indicators of metabolic disorders rather than more severe obesity. The PICRUSt analysis demonstrated 70 significantly different microbiome community functions between the two groups, which were mainly involved in carbohydrate and amino acid metabolism, such as promoting Arachidonic acid metabolism, mineral absorption, and Lipopolysaccharide biosynthesis, reducing Arginine and proline metabolism, flavone and flavonol biosynthesis, Glycolysis/Gluconeogenesis, and primary bile acid biosynthesis. Furthermore, a disease classifier based on microbiota was constructed to accurately discriminate PDC individuals from all obese people.

Conclusion

Our study shows that obese individuals with PDC can be distinguished from non-PDC obese individuals based on gut microbial characteristics. The composition of the gut microbiome altered in obese with PDC may be responsible for their high risk of metabolic diseases.

Lactobacillus kefiranofaciens JKSP109 and Saccharomyces cerevisiae JKSP39 isolated from Tibetan kefir grain co-alleviated AOM/DSS induced inflammation and colorectal carcinogenesis

This study aimed to investigate the alleviative effects of Lactobacillus kefiranofaciens JKSP109 (LK) and Saccharomyces cerevisiae JKSP39 (SC) isolated from Tibetan kefir grain on colon inflammation and colorectal carcinogenesis. Azoxymethane (AOM) and dextran sulfate sodium (DSS) were used to establish a mouse model of colorectal cancer (CRC). The treatment group mice were administered with LK, SC, or the combination of LK and SC for five days per week from the day of receiving AOM. The composition of the gut microbiota was assessed using internal transcribed spacer 2 and 16S rRNA gene high-throughput sequencing. Furthermore, the biomarkers associated with gut barrier integrity, inflammation, regulators of cell proliferation, and apoptosis were evaluated. The results showed that the administration of LK, SC, and their combination increased the body weights and decreased the disease activity index (DAI) score and tumor multiplicity. As compared to the CRC model group, the three treatment groups positively regulated the gut microbiota. Meanwhile, the three treatments also enhanced the gut barrier, decreased the expression of proinflammatory cytokines and oncocyte proliferation indicators, and increased the expression of terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL)-positive tumor epithelial cells and content of short chain fatty acids in fecal samples. All these results indicated that the LK and SC alleviated the inflammation and colorectal carcinogenesis in AOM/DSS-induced CRC mouse models, and the majority of tested indexes in the combination group were superior to single strain groups.

Rubus chingii Hu. unripe fruits extract ameliorates carbon tetrachloride-induced liver fibrosis and improves the associated gut microbiota imbalance

BACKGROUND

The unripe fruits of Rubus chingii Hu. ("Fu-peng-zi" in Chinese) is a well-known herbal tonic in traditional Chinese medicine (TCM) for tonifying liver and kidney. However, little is known regarding its therapeutic efficacy against liver fibrosis and the underlying mechanism.

METHODS

The current research aims to explore the potential of Rubus chingii Hu. unripe fruits extract (RF) in the treatment of liver fibrosis and explore the underlying mechanism. RF was administered (450 and 900 mg·kg^- 1 of body weight per day) orally to male C57BL/6 mice with CCl₄-induced liver fibrosis for 3 weeks. The histopathological changes and fibrosis stage in liver tissue were assessed using hematoxylin and eosin (H&E) and Sirius red staining. The distribution of α-SMA and Col1A1 in the liver was analyzed to determine the hepatic stellate cells (HSCs) activation using immunohistochemistry and immunofluorescent analysis. Various biochemical markers in serum (ALT, AST) and liver (Hyp, IL1-β, IL6, TNF-α and MCP-1) were observed to assess the liver's injury, fibrosis, and inflammation. In liver tissue, fibrosis-associated proteins including α-SMA, TGF-β1, Smad2/3, p-Smad2/3, and Smad4 were detected through a Western blot assay. Pyrosequencing-based analysis of bacterial 16 S ribosomal RNA from variable regions V3-V4 of fecal samples characterized the gut microbiota. Spearman's rank correlation analysis was performed for the association between altered bacterial genera by RF and pharmacodynamics parameters.

RESULTS

Three weeks of RF treatment can significantly lower liver inflammatory levels, pathological abnormalities, and collagen fibrous deposition in mice with CCl₄-induced liver fibrosis. The expressions of α-SMA and Col1A1 were lowered by RF, while the expression levels of TGF-β/Smads signaling pathway-related proteins, including TGF-β1, p-Smad2/3, and Smad4, were dramatically decreased by RF. The RF treatment significantly increased or reduced 18 different bacterial species, restoring the CCl₄-induced gut microbiota imbalance to the normal group's levels. According to correlation analysis, the bacterial genera Bifidobacterium and Turicibacter were the most significant in restoring CCl₄-induced liver fibrosis.

CONCLUSIONS

RF can reduce liver damage and delay the onset of liver fibrosis through modulating TGF-β/Smads signaling pathway. Furthermore, RF's anti-liver fibrosis effect was related to balancing the gut microbial community, partly attained by increasing Bifidobacterium and Turicibacter in liver fibrosis.

Understanding the Role of the Microbiome in Cancer Diagnostics and Therapeutics by Creating and Utilizing ML Models

Recent studies have highlighted that gut microbiota can alter colorectal cancer susceptibility and progression due to its impact on colorectal carcinogenesis. This work represents a comprehensive technical approach in modeling and interpreting the drug-resistance mechanisms from clinical data for patients diagnosed with colorectal cancer. To accomplish our aim, we developed a methodology based on evaluating high-performance machine learning models where a Python-based random forest classifier provides the best performance metrics, with an overall accuracy of 91.7%. Our approach identified and interpreted the most significant genera in the cases of resistant groups. Thus far, many studies point out the importance of present genera in the microbiome and intend to treat it separately. The symbiotic bacterial analysis generated different sets of joint feature combinations, providing a combined overview of the model’s predictiveness and uncovering additional data correlations where different genera joint impacts support the therapy-resistant effect. This study points out the different perspectives of treatment since our aggregate analysis gives precise results for the genera that are often found together in a resistant group of patients, meaning that resistance is not due to the presence of one pathogenic genus in the patient microbiome, but rather several bacterial genera that live in symbiosis.

Restoration of the gut microbiota is associated with a decreased risk of hepatic encephalopathy after TIPS

Background & Aims

Hepatic encephalopathy (HE) is a major complication after transjugular intrahepatic portosystemic shunt (TIPS) and is primarily influenced by the gut microbiota. We aimed to evaluate alterations in the microbiota after TIPS and the association between such alterations and HE.

Methods

We conducted a prospective longitudinal study of 106 patients with cirrhosis receiving TIPS. Faecal samples were collected before and after TIPS, and the gut microbiota was analysed by 16S ribosomal RNA sequencing.

Results

Among all patients, 33 developed HE (HE+ group) within 6 months after TIPS and 73 did not (HE- group), and 18 died during follow-up. After TIPS, the autochthonous taxa increased, whereas the potential pathogenic taxa decreased in the HE- group, and the autochthonous taxon Lachnospiraceae decreased in the HE+ group. Furthermore, synergism among harmful bacteria was observed in all patients, which was weakened in the HE- group (p <0.001) but enhanced in the HE+ group (p <0.01) after TIPS. Variations of 5 autochthonous taxa, namely, Coprococcus, Ruminococcus, Blautia, Ruminococcaceae_uncultured, and Roseburia, were negatively correlated with the severity of HE. Notably, increased abundances of Coprococcus and Ruminococcus were protective factors against HE, and the incidences of HE in patients with improved, stable, and deteriorated microbiota after TIPS were 13.3, 25.9, and 68.2%, respectively. Higher total bilirubin level, Child–Pugh score, model for end-stage liver disease score, Granulicatella, and Alistipes and lower Subdoligranulum before TIPS were the independent risk factors for death.

Conclusions

Alterations in gut dysbiosis were negatively related to the occurrence and severity of post-TIPS HE, and the pre-TIPS microbiota were associated with death, suggesting the gut microbiota could be a promising potential biological target for screening suitable patients receiving TIPS and prevention and treatment of post-TIPS HE.

Lay summary

Alterations in the gut microbiota after transjugular intrahepatic portosystemic shunt (TIPS) and the relationship between such alterations and post-TIPS hepatic encephalopathy (HE) remain unclear. We therefore performed this study and found that after TIPS, restoration of the gut microbiota, mainly characterised by expansion of autochthonous taxa, depletion of harmful taxa, and weakening of synergism among harmful bacteria, was inversely related to the occurrence and severity of post-TIPS HE.

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Gut dysbiosis of the patients without HE showed significant improvement after TIPS.

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Expansion of autochthonous taxa after TIPS was negatively correlated with the occurrence and severity of HE.

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The changes of relationship among the microbiota in different prognostic groups were opposite.

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Pre-TIPS gut microbiota and certain clinical indices were associated with survival.

CACONET: a novel classification framework for microbial correlation networks

MOTIVATION

Existing microbiome-based disease prediction relies on the ability of machine learning methods to differentiate disease from healthy subjects based on the observed taxa abundance across samples. Despite numerous microbes have been implicated as potential biomarkers, challenges remain due to not only the statistical nature of microbiome data but also the lack of understanding of microbial interactions which can be indicative of the disease.

RESULTS

We propose CACONET (classification of Compositional-Aware COrrelation NETworks), a computational framework that learns to classify microbial correlation networks and extracts potential signature interactions, taking as input taxa relative abundance across samples and their health status. By using Bayesian compositional-aware correlation inference, a collection of posterior correlation networks can be drawn and used for graph-level classification, thus incorporating uncertainty in the estimates. CACONET then employs a deep learning approach for graph classification, achieving excellent performance metrics by exploiting the correlation structure. We test the framework on both simulated data and a large real-world dataset pertaining to microbiome samples of colorectal cancer (CRC) and healthy subjects, and identify potential network substructure characteristic of CRC microbiota. CACONET is customizable and can be adapted to further improve its utility.

AVAILABILITY AND IMPLEMENTATION

CACONET is available at https://github.com/yuanwxu/corr-net-classify.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A prognostic fibroblast-related risk signature in colorectal cancer

Colorectal cancer (CRC) is the third most common cancer in the world. The accessibility of the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus data allows the prognostic evaluation of CRC. Fibroblasts play a key role in the development and progression of tumors while fibroblast-related risk signature in CRC patients has rarely been mentioned. In this study, TCGA data was classified into high-fibroblast and low-fibroblast groups according to the median of fibroblast content. Among 3845 differentially expressed genes between two groups, 14 prognostic genes commonly expressed in GSE39582 and TCGA were identified by LASSO-COX analysis. Then we established a fibroblast-related risk signature in TCGA training group and validated in the GSE39582 testing group. The risk score was significantly associated with the overall survival (OS), and the poor prognosis of patients in high-risk group might relate to the immune cell infiltration in the tumor microenvironment, epithelial-mesenchymal transition, and extracellular matrix related processes. Overall, we proved that the fibroblast-related signature could predict the prognosis of patients which might shed light on the treatment of CRC.

Recent advances in utilization of pectins in biomedical applications: a review focusing on molecular structure-directing health-promoting properties

The numerous health benefits of pectins justify their inclusion in human diets and biomedical products. This review provides an overview of pectin extraction and modification methods, their physico-chemical characteristics, health-promoting properties, and pharmaceutical/biomedical applications. Pectins, as readily available and versatile biomolecules, can be tailored to possess specific functionalities for food, pharmaceutical and biomedical applications, through judicious selection of appropriate extraction and modification technologies/processes based on green chemistry principles. Pectin's structural and physicochemical characteristics dictate their effects on digestion and bioavailability of nutrients, as well as health-promoting properties including anticancer, immunomodulatory, anti-inflammatory, intestinal microflora-regulating, immune barrier-strengthening, hypercholesterolemia-/arteriosclerosis-preventing, anti-diabetic, anti-obesity, antitussive, analgesic, anticoagulant, and wound healing effects. HG, RG-I, RG-II, molecular weight, side chain pattern, and degrees of methylation, acetylation, amidation and branching are critical structural elements responsible for optimizing these health benefits. The physicochemical characteristics, health functionalities, biocompatibility and biodegradability of pectins enable the construction of pectin-based composites with distinct properties for targeted applications in bioactive/drug delivery, edible films/coatings, nano-/micro-encapsulation, wound dressings and biological tissue engineering. Achieving beneficial synergies among the green extraction and modification processes during pectin production, and between pectin and other composite components in biomedical products, should be key foci for future research.

Association of Polygenic Risk Score and Bacterial Toxins at Screening Colonoscopy with Colorectal Cancer Progression: A Multicenter Case-Control Study

Colorectal cancer (CRC) is a leading cause of cancer death worldwide, and its incidence is correlated with infections, chronic inflammation, diet, and genetic factors. An emerging aspect is that microbial dysbiosis and chronic infections triggered by certain bacteria can be risk factors for tumor progression. Recent data suggest that certain bacterial toxins implicated in DNA attack or in proliferation, replication, and death can be risk factors for insurgence and progression of CRC. In this study, we recruited more than 300 biopsy specimens from people undergoing colonoscopy, and we analyzed to determine whether a correlation exists between the presence of bacterial genes coding for toxins possibly involved in CRC onset and progression and the different stages of CRC. We also analyzed to determine whether CRC-predisposing genetic factors could contribute to bacterial toxins response. Our results showed that CIF toxin is associated with polyps or adenomas, whereas pks+ seems to be a predisposing factor for CRC. Toxins from Escherichia coli as a whole have a higher incidence rate in adenocarcinoma patients compared to controls, whereas Bacteroides fragilis toxin does not seem to be associated with pre-cancerous nor with cancerous lesions. These results have been obtained irrespectively of the presence of CRC-risk loci.

Lights and Shadows of Microbiota Modulation and Cardiovascular Risk in HIV Patients

Human immunodeficiency virus (HIV) infection is associated with premature aging and the development of aging-related comorbidities, such as cardiovascular disease (CVD). Gut microbiota (GM) disturbance is involved in these comorbidities and there is currently interest in strategies focused on modulating GM composition and/or functionality. Scientific evidence based on well-designed clinical trials is needed to support the use of prebiotics, probiotics, symbiotics, and fecal transplantation (FT) to modify the GM and reduce the incidence of CVD in HIV-infected patients. We reviewed the data obtained from three clinical trials focused on prebiotics, 25 trials using probiotics, six using symbiotics, and four using FT. None of the trials investigated whether these compounds could reduce CVD in HIV patients. The huge variability observed in the type of compound as well as the dose and duration of administration makes it difficult to adopt general recommendations and raise serious questions about their application in clinical practice.

Dietary pectic substances enhance gut health by its polycomponent: A review

Pectic substances, one of the cell wall polysaccharides, exist widespread in vegetables and fruits. A surge of recent research has revealed that pectic substances can inhibit gut inflammation and relieve inflammatory bowel disease symptoms. However, physiological functions of pectins are strongly structure dependent. Pectic substances are essentially heteropolysaccharides composed of homogalacturonan and rhamnogalacturonan backbones substituted by various neutral sugar sidechains. Subtle changes in the architecture of pectic substances may remarkably influence the nutritional function of gut microbiota and the host homeostasis of immune system. In this context, developing a structure-function understanding of how pectic substances have an impact on an inflammatory bowel is of primary importance for diet therapy and new drugs. Therefore, the present review has summarized the polycomponent nature of pectic substances, the activities of different pectic polymers, the effects of molecular characteristics and the underlying mechanisms of pectic substances. The immunomodulated property of pectic substances depends on not only the chemical composition but also the physical structure characteristics, such as molecular weight (M_w ) and chain conformation. The potential mechanisms by which pectic substances exert their protective effects are mainly reversing the disordered gut microbiota, regulating immune cells, enhancing barrier function, and inhibiting pathogen adhesion. The manipulation of pectic substances on gut health is sophisticated, and the link between structural specificity of pectins and selective regulation needs further exploration.

The Distinctive Serum Metabolomes of Gastric, Esophageal and Colorectal Cancers

Simple Summary

Cancer of the stomach, esophagus and colon are often fatal. Ways are being sought to establish patient-friendly screening tests that would allow these cancers to be detected earlier. Examination of the metabolomics results of cancer patient’s serum for certain metabolites unique for a particular cancer was the goal of this review. From studies conducted within the past five years several metabolites were found to be changed in cancer compared to non-cancer patients for each of the three cancers. Further confirmation of what was discovered in this review coupled with establishment of standard protocols may allow for cancer screening on patient blood samples to become routine clinical tests.

Abstract

Three of the most lethal cancers in the world are the gastrointestinal cancers—gastric (GC), esophageal (EC) and colorectal cancer (CRC)—which are ranked as third, sixth and fourth in cancer deaths globally. Early detection of these cancers is difficult, and a quest is currently on to find non-invasive screening tests to detect these cancers. The reprogramming of energy metabolism is a hallmark of cancer, notably, an increased dependence on aerobic glycolysis which is often referred to as the Warburg effect. This metabolic change results in a unique metabolic profile that distinguishes cancer cells from normal cells. Serum metabolomics analyses allow one to measure the end products of both host and microbiota metabolism present at the time of sample collection. It is a non-invasive procedure requiring only blood collection which encourages greater patient compliance to have more frequent screenings for cancer. In the following review we will examine some of the most current serum metabolomics studies in order to compare their results and test a hypothesis that different tumors, notably, from EC, GC and CRC, have distinguishing serum metabolite profiles.