Search

Supplementary figures

Table S5

Table S7

Table S6

Table S2

Table S3

Table S1

Purpose:Intratumoral hepatitis B virus (HBV) integrations and mutations are related to hepatocellular carcinoma (HCC) progression. Circulating cell-free DNA (cfDNA) has shown itself as a powerful noninvasive biomarker for cancer. However, the HBV integration and mutation landscape on cfDNA remains unclear.Experimental Design:A cSMART (Circulating Single-Molecule Amplification and Resequencing Technology)-based method (SIM) was developed to simultaneously investigate HBV integration and mutation landscapes on cfDNA with HBV-specific primers covering the whole HBV genome. Patients with HCC (n = 481) and liver cirrhosis (LC; n = 517) were recruited in the study.Results:A total of 6,861 integration breakpoints including TERT and KMT2B were discovered in HCC cfDNA, more than in LC. The concentration of circulating tumor DNA (ctDNA) was positively correlated with the detection rate of these integration hotspots and total HBV integration events in cfDNA. To track the origin of HBV integrations in cfDNA, whole-genome sequencing (WGS) was performed on their paired tumor tissues. The paired comparison of WGS data from tumor tissues and SIM data from cfDNA confirmed most recurrent integration events in cfDNA originated from tumor tissue. The mutational landscape across the whole HBV genome was first generated for both HBV genotype C and B. A region from nt1100 to nt1500 containing multiple HCC risk mutation sites (OR > 1) was identified as a potential HCC-related mutational hot zone.Conclusions:Our study provides an in-depth delineation of HBV integration/mutation landscapes at cfDNA level and did a comparative analysis with their paired tissues. These findings shed light on the possibilities of noninvasive detection of virus insertion/mutation.

Table S4

Background Hepatocellular carcinoma (HCC) generally arises from a background of liver cirrhosis (LC). Patients with cirrhosis and suspected HCC are recommended to undergo serum biomarker tests and imaging diagnostic evaluation. However, the performance of routine diagnostic methods in detecting early HCC remains unpromising. Methods Here, we conducted a large-scale, multicenter study of 1675 participants including 490 healthy controls, 577 LC patients, and 608 HCC patients from nine clinical centers across nine provinces of China, profiled gene mutation signatures of cell-free DNA (cfDNA) using Circulating Single-Molecule Amplification and Resequencing Technology (cSMART) through detecting 931 mutation sites across 21 genes. Results An integrated diagnostic model called “Combined method” was developed by combining three mutation sites and three serum biomarkers. Combined method outperformed AFP in the diagnosis of HCC, especially early HCC, with sensitivities of 81.25% for all stages and 66.67% for early HCC, respectively. Importantly, the integrated model exhibited high accuracy in differentiating AFP-negative, AFP-L3-negative, and PIVKA-II-negative HCCs from LCs.

Background:. The basis of individualized treatment should be individualized mortality risk predictive information. The present study aimed to develop an online individual mortality risk predictive tool for acute-on-chronic liver failure (ACLF) patients based on a random survival forest (RSF) algorithm. Methods:. The current study retrospectively enrolled ACLF patients from the Department of Infectious Diseases of The First People's Hospital of Foshan, Shunde Hospital of Southern Medical University, and Jiangmen Central Hospital. Two hundred seventy-six consecutive ACLF patients were included in the present study as a model cohort (n = 276). Then the current study constructed a validation cohort by drawing patients from the model dataset based on the resampling method (n = 276). The RSF algorithm was used to develop an individual prognostic model for ACLF patients. The Brier score was used to evaluate the diagnostic accuracy of prognostic models. The weighted mean rank estimation method was used to compare the differences between the areas under the time-dependent ROC curves (AUROCs) of prognostic models. Results:. Multivariate Cox regression identified hepatic encephalopathy (HE), age, serum sodium level, acute kidney injury (AKI), red cell distribution width (RDW), and international normalization index (INR) as independent risk factors for ACLF patients. A simplified RSF model was developed based on these previous risk factors. The AUROCs for predicting 3-, 6-, and 12-month mortality were 0.916, 0.916, and 0.905 for the RSF model and 0.872, 0.866, and 0.848 for the Cox model in the model cohort, respectively. The Brier scores were 0.119, 0.119, and 0.128 for the RSF model and 0.138, 0.146, and 0.156 for the Cox model, respectively. The nonparametric comparison suggested that the RSF model was superior to the Cox model for predicting the prognosis of ACLF patients. Conclusions:. The current study developed a novel online individual mortality risk predictive tool that could predict individual mortality risk predictive curves for individual patients. Additionally, the current online individual mortality risk predictive tool could further provide predicted mortality percentages and 95% confidence intervals at user-defined time points.

Purpose: Intratumoral hepatitis B virus (HBV) integrations and mutations are related to hepatocellular carcinoma (HCC) progression. Circulating cell-free DNA (cfDNA) has shown itself as a powerful noninvasive biomarker for cancer. However, the HBV integration and mutation landscape on cfDNA remains unclear. Experimental Design: A cSMART (Circulating Single-Molecule Amplification and Resequencing Technology)-based method (SIM) was developed to simultaneously investigate HBV integration and mutation landscapes on cfDNA with HBV-specific primers covering the whole HBV genome. Patients with HCC (n = 481) and liver cirrhosis (LC; n = 517) were recruited in the study. Results: A total of 6,861 integration breakpoints including TERT and KMT2B were discovered in HCC cfDNA, more than in LC. The concentration of circulating tumor DNA (ctDNA) was positively correlated with the detection rate of these integration hotspots and total HBV integration events in cfDNA. To track the origin of HBV integrations in cfDNA, whole-genome sequencing (WGS) was performed on their paired tumor tissues. The paired comparison of WGS data from tumor tissues and SIM data from cfDNA confirmed most recurrent integration events in cfDNA originated from tumor tissue. The mutational landscape across the whole HBV genome was first generated for both HBV genotype C and B. A region from nt1100 to nt1500 containing multiple HCC risk mutation sites (OR > 1) was identified as a potential HCC-related mutational hot zone. Conclusions: Our study provides an in-depth delineation of HBV integration/mutation landscapes at cfDNA level and did a comparative analysis with their paired tissues. These findings shed light on the possibilities of noninvasive detection of virus insertion/mutation.

Background: Patients with liver cirrhosis are at higher risk of developing hepatocellular carcinoma (HCC). Due to the low accuracy of current methods, new non-invasive strategies for early HCC diagnosis in cirrhotic patients are needed. Methods: A case-control study recruited a total of 2,250 patients with liver cirrhosis (LC), 508 with HCC, and 476 healthy controls (CTRL), from 13 hospitals in 11 provinces of China. Four genomic features of cell-free DNA (cfDNA), including nucleosome footprint, fragmentation, base mismatch and 5-hydroxymethylcytosines were profiled. Training and validation cohorts helped develop the integrated diagnostic model, and a test cohort was used to evaluate its performance. Findings: We established a classifier of each feature for HCC against non-HCC (cirrhosis & healthy control). By integrating these four genomic features, we developed a novel diagnostic model (HIFI, 5-Hydroxymethylcytosines/base mIsmatch/Fragmentation/nucleosome footprInt), and achieved a higher accuracy in differentiating HCCs from liver cirrhosis (AUC=0.997 [0.994-0.999], sensitivity 95.42%, specificity 97.67% in test set) than AFP or PIVKA-II, irrespective of the following demographics and clinical features, age, HBV status, Child-Pugh score, BCLC stage, tumor size, and AFP status. In AFP positive (AFP>20ug/L) liver cirrhosis patients and AFP/PIVKA-II negative (AFP 400μg/L: 100% in liver cirrhosis patients; AFP

Background. We aimed to determine a discriminant function for prognosis in chronic severe hepatitis B (CSHB), by discriminant analysis of prognostic indexes and probability of death. Methods. In 205 patients with chronic severe hepatitis B (101 patients in the survival group and 104 patients in the death group), we carried out discriminant analysis of serum total bilirubin, prothrombin activity, white blood cells, creatinine, maximum depth of ascites, hepatic encephalopathy, singultus, and digestive tract hemorrhage. Results. The discriminant function was V = 0.00043 × total bilirubin (µM) − 0.025 × prothrombin activity (%) + 0.056 × white blood cells (109/l) + 0.00284 × creatinine (µM) + 0.0014 × maximum depth of ascites (mm) + 0.724 × hepatic encephalopathy score + 0.078 × singultus score + 0.457 × digestive tract hemorrhage score − 2.488. The correctness of the function for predicting death in the death group was 92.3%, and that for predicting survival in the survival group was 96.0%. When the V values were −∞, −4.595, −2.197, −1.386, −0.405, 0.405, 1.386, 2.197, 2.944, 4.595, and ∞, a posterior probabilities of death were 0%, 5%, 10%, 20%, 40%, 60%, 80%, 90%, 95%, 99%, and 100%, respectively. Conclusions. The discriminant function is an objective, convenient, and practical method to assess the prognosis of chronic severe hepatitis B.

Although regulatory T cells (Treg) and interleukin-17-producing CD4 T cells (Th17) have been demonstrated to play opposing roles in inflammation-associated diseases, their frequency and balance in different stages of hepatitis B virus (HBV)-related acute-on-chronic liver failure (ACLF) remain unknown.Fourteen patients with HBV-associated ACLF were studied and defined into different stages according to disease activity. Circulating Th17 cells and Treg cells were analyzed by flow cytometry, and the cytokines were quantitated by enzyme-linked immunosorbent assay. Results were correlated with temporal changes in viral load, disease progression and compared with 30 chronic hepatitis B (CHB) subjects and 18 healthy subjects.We showed a significantly higher frequency of circulating Th17 cells in the remission stage of ACLF when compared with the progression stage, the CHB group, or normal controls. However, the frequency of circulating Treg cells was significantly lower in the remission stage of ACLF when compared with the progression stage or the CHB group. The increase in Th17 cells and concomitant decrease in Treg cells created an imbalance in the remission stage of ACLF patients, which negatively correlated with disease progression. In addition, we showed that ACLF patients in the remission stage had an altered profile of cytokines that regulated the induction of Th17 cells and Treg cells.ACLF patients in the remission stage had an imbalance of Th17 to Treg cells, which could be used as a prognostic marker to predict disease progression. This imbalance could play a role in the immunopathogenesis of HBV-related ACLF.

To study the clinical efficacy of three kinds of hybrid bioartificial liver support systems (HBLSS) in treating chronic severe hepatitis.A bioartificial liver support system (BAL), comprising porcine hepatocytes and fiber tube style bioreactor, was constructed. Then three kinds of HBLSS were constructed: Molecular absorbent recirculating system (MARS) plus BAL; slow plasma exchange (SPE) plus continuous hemodiafiltration (CHDF) and BAL; and SPE plus hemoperfusion (HP) and BAL. One hundred-twenty patients in middle or late stages of chronic severe hepatitis were enrolled in this study. They were randomly divided into 6 groups: H1 group was treated with BAL+MARS, H2 with BAL+SPE+CHDF and H3 with BAL+SPE+HP (as treatment groups); C1 group was treated with MARS, C2 with SPE+CHDF and C3 with SPE+HP (as control groups). The changes in the clinical symptoms, in the hepatic encephalopathy stages, and in the serum total bilirubin (TBIL), the serum albumin (ALB), the prothrombin activities (PTA), endotoxin, ammonia, creatinine and a-fetal protein (AFP) were all observed before the treatment, right after it and 72 hours later. The improving and curing rates and the rates of side effect occurrences in each group were observed.In all 6 groups, the patients' clinical symptoms ameliorated; their TBIL, endotoxin and ammonia levels decreased (P0.05), and their PTA and AFP levels lowered significantly (P0.05). But in the H1, H2 and H3 groups they were more distinctive than in the control groups. In H1 and H2 groups creatinine and ammonia levels were decreased more significantly than in the H3 group (P0.05). The improving and curing rates of each group were 65 % (13/20), 60% (12/20), 45% (9/20), 45% (9/20), 40% (8/20) and 20% (4/20) respectively. No serious side effects were observed during the treatment.In treating middle and late stage chronic severe hepatitis, the measures used in H1, H2 and H3 are better than those in C1, C2 and C3. Furthermore, H1 and H2 treatments can ameliorate hepatic and renal functions, prevent the development of multiple organ dysfunction syndrome, and are better than those used in H3.