Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients

Viruses are the most abundant form of life on earth and play important roles in a broad range of ecosystems. Currently, two methods, whole genome shotgun metagenome (WGSM) and viral-like particle enriched metagenome (VLPM) sequencing, are widely applied to compare viruses in various environments. However, there is no critical assessment of their performance in recovering viruses and biological interpretation in comparative viral metagenomic studies. To fill this gap, we applied the two methods to investigate the stool virome in hepatocellular carcinoma (HCC) patients and healthy controls. Both WGSM and VLPM methods can capture the major diversity patterns of alpha and beta diversities and identify the altered viral profiles in the HCC stool samples compared with healthy controls. Viral signatures identified by both methods showed reductions of Faecalibacterium virus Taranis in HCC patients' stool. Ultra-deep sequencing recovered more viruses in both methods, however, generally, 3 or 5 Gb were sufficient to capture the non-fragmented long viral contigs. More lytic viruses were detected than lysogenetic viruses in both methods, and the VLPM can detect the RNA viruses. Using both methods would identify shared and specific viral signatures and would capture different parts of the total virome.

Refining a Protocol for Faecal Microbiota Engraftment in Animal Models After Successful Antibiotic-Induced Gut Decontamination

Background

There is mounting evidence for the therapeutic use of faecal microbiota transplant (FMT) in numerous chronic inflammatory diseases. Germ free mice are not always accessible for FMT research and hence alternative approaches using antibiotic depletion prior to FMT in animal studies are often used. Hence, there is a need for standardising gut microbiota depletion and FMT methodologies in animal studies. The aim of this study was to refine gut decontamination protocols prior to FMT engraftment and determine efficiency and stability of FMT engraftment over time.

Methods

Male C57BL/6J mice received an antibiotic cocktail consisting of ampicillin, vancomycin, neomycin, and metronidazole in drinking water for 21 days ad libitum. After antibiotic treatment, animals received either FMT or saline by weekly oral gavage for 3 weeks (FMT group or Sham group, respectively), and followed up for a further 5 weeks. At multiple timepoints throughout the model, stool samples were collected and subjected to bacterial culture, qPCR of bacterial DNA, and fluorescent in-situ hybridisation (FISH) to determine bacterial presence and load. Additionally, 16S rRNA sequencing of stool was used to confirm gut decontamination and subsequent FMT engraftment.

Results

Antibiotic treatment for 7 days was most effective in gut decontamination, as evidenced by absence of bacteria observed in culture, and reduced bacterial concentration, as determined by FISH as well as qPCR. Continued antibiotic administration had no further efficacy on gut decontamination from days 7 to 21. Following gut decontamination, 3 weekly doses of FMT was sufficient for the successful engraftment of donor microbiota in animals. The recolonised animal gut microbiota was similar in composition to the donor sample, and significantly different from the Sham controls as assessed by 16S rRNA sequencing. Importantly, this similarity in composition to the donor sample persisted for 5 weeks following the final FMT dose.

Conclusions

Our results showed that 7 days of broad-spectrum antibiotics in drinking water followed by 3 weekly doses of FMT provides a simple, reliable, and cost-effective methodology for FMT in animal research.

Non-alcoholic fatty liver disease: a review of epidemiology, risk factors, diagnosis and management

Due to the rising prevalence of obesity and type II diabetes mellitus, non-alcoholic fatty liver disease is becoming the leading cause of chronic liver disease in the Western world. In some patients, simple steatosis can result in non-alcoholic steatohepatitis which over time can lead to liver cirrhosis and its associated sequelae, including hepatocellular carcinoma. Early identification and management of patients at risk with intensive dietary and lifestyle modification are essential to prevent the development of advanced liver disease and its complications. In this review, we will discuss the epidemiology of non-alcoholic fatty liver disease, pathogenesis, diagnosis, management and surveillance strategies to offset the morbidity and mortality of this disease, as well as liver and non-liver-related complications.

Defining the temporal evolution of gut dysbiosis and inflammatory responses leading to hepatocellular carcinoma in Mdr2 -/- mouse model

BACKGROUND

Emerging evidence implicates the gut microbiome in liver inflammation and hepatocellular carcinoma (HCC) development. We aimed to characterize the temporal evolution of gut dysbiosis, in relation to the phenotype of systemic and hepatic inflammatory responses leading to HCC development. In the present study, Mdr2 -/- mice were used as a model of inflammation-based HCC. Gut microbiome composition and function, in addition to serum LPS, serum cytokines/chemokines and intrahepatic inflammatory genes were measured throughout the course of liver injury until HCC development.

RESULTS

Early stages of liver injury, inflammation and cirrhosis, were characterized by dysbiosis. Microbiome functional pathways pertaining to gut barrier dysfunction were enriched during the initial phase of liver inflammation and cirrhosis, whilst those supporting lipopolysaccharide (LPS) biosynthesis increased as cirrhosis and HCC ensued. In parallel, serum LPS progressively increased during the course of liver injury, corresponding to a shift towards a systemic Th1/Th17 proinflammatory phenotype. Alongside, the intrahepatic inflammatory gene profile transitioned from a proinflammatory phenotype in the initial phases of liver injury to an immunosuppressed one in HCC. In established HCC, a switch in microbiome function from carbohydrate to amino acid metabolism occurred.

CONCLUSION

In Mdr2 -/- mice, dysbiosis precedes HCC development, with temporal evolution of microbiome function to support gut barrier dysfunction, LPS biosynthesis, and redirection of energy source utilization. A corresponding shift in systemic and intrahepatic inflammatory responses occurred supporting HCC development. These findings support the notion that gut based therapeutic interventions could be beneficial early in the course of liver disease to halt HCC development.

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma

The gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.

The interobserver agreement of optical features used to differentiate benign from neoplastic biliary lesions assessed at balloon-assisted cholangioscopy

BACKGROUND AND AIM

Balloon-assisted cholangioscopy allows mucosal assessment of the biliary tree with pediatric endoscopes. No validated optical criteria exist to differentiate benign from neoplastic biliary lesions. We aimed to identify, validate, and revalidate optical features differentiating benign from neoplastic biliary lesions. Furthermore, we aimed to determine whether cholangioscopic appearance allows endoscopists to accurately differentiate benign from neoplastic biliary lesions.

METHODS

Baseline: from 44 de-identified balloon-assisted cholangioscopy videos, a blinded investigator analyzed potential optical features distinguishing benign from neoplastic biliary lesions.

VALIDATION

during the initial "teaching phase," 20 endoscopists viewed video clips of 11 optical features identified in the baseline study. At the subsequent "test phase," 20 further video clips were assessed by the endoscopists blinded to clinical details and questionnaires completed for the presence or absence of optical features, favored diagnosis and diagnostic confidence. Revalidation: The six identified optical features from the validation study with at least moderate agreement were revalidated the same way 12 months later assessing 20 new lesions.

RESULTS

Baseline: 11 optical features were found to differentiate benign from neoplastic biliary lesions. Validation and revalidation: six optical features demonstrated at least moderate interobserver agreement (irregular margin, dark mucosa, adherent mucous, papillary projections, tubular, or branched/disorganized surface structures). Endoscopists correctly diagnosed lesions as benign in 89% and neoplastic in 83%. When highly confident, endoscopists correctly diagnosed 96% of benign and 87% neoplastic lesions.

CONCLUSIONS

Six features were validated and revalidated to differentiate benign from neoplastic biliary lesions. When highly confident with a diagnosis, endoscopists usually differentiate benign from neoplastic biliary lesions.

Prevalence of adenomas and sessile serrated adenomas in Chinese compared with Caucasians

BACKGROUND AND AIMS

Colonic adenomas and sessile serrated adenomas (SSA) are the most common premalignant polyps identified at colonoscopy. This study compares the prevalence of neoplastic polyps in Chinese and Caucasians in a general gastroenterology outpatient practice in Australia.

METHODS

This study included consecutive unselected colonoscopies performed for standard clinical indications by a single endoscopist (JMH). All polyps detected were measured, resected, and sent for histopathology. The prevalence of adenomas, advanced adenomas, SSA, and cancer in the Chinese and Caucasian cohorts were compared. Advanced adenomas were defined as adenomas > 10 mm, villous histology, or high-grade dysplasia.

RESULTS

The study included 346 Chinese and 654 Caucasians. There was no significant difference in the baseline characteristics including age, gender, and indications of colonoscopy, although Chinese were more likely to present with rectal bleeding (22.8% vs 15.9%, P = 0.01). The prevalence of adenomatous polyps was similar in both Caucasians (34.3%) and Chinese (35.3%). However, advanced adenomas were more significantly common in Caucasians (11.3%) compared with Chinese (4.6%) (P < 0.001). SSA was rare in Chinese (2%) but present more frequently in Caucasians (7%) (P = 0.001). Multivariate analysis showed that Caucasian ethnicity (odds ratio 2.4, 95% confidence interval 1.6-3.6) and the presence of SSA (odds ratio 4.4, 95% confidence interval 2.3-8.6) were independent predictors for the detection of an advanced adenoma.

CONCLUSIONS

The prevalence of significant colorectal lesions, including advanced adenomas, large adenomas, and SSA, were lower in Chinese compared with Caucasians. These findings may influence the guidelines for colonic cancer screening in Chinese populations.