Inheritance of Histones H3 and H4 during DNA Replication In Vitro

Summary: Nucleosomes are believed to carry epigenetic information through the cell cycle, including through DNA replication. It has been known for decades that parental histones are reassembled on newly replicated chromatin, but the mechanisms underlying histone inheritance and dispersal during DNA replication are not fully understood. We monitored the fate of histones H3 or H4 from a single nucleosome through DNA replication in two in vitro systems. In the SV40 system, histones assembled on a single nucleosome positioning sequence can be inherited by their own daughter DNA but are dispersed from their original location. In Xenopus laevis extracts, histones are dynamic, and nucleosomes are repositioned independent of and prior to DNA replication. Nevertheless, a high fraction of histones H3 and H4 that are inherited through DNA replication remains near its starting location. Thus, inheritance of histone proteins and their dispersal can be mechanistically uncoupled. : Chromatin-based information, including that carried by histones, must be copied when DNA is replicated. By tracking histones H3 or H4 from a single nucleosome through DNA replication in two in vitro systems, Madamba et al. identify two modes of histone inheritance, one of which preserves genomic positioning information. Keywords: epigenetic, histones, chromatin, DNA replication, SV40, Xenopus laevi

Diagnostic accuracy of two-dimensional shear wave elastography and transient elastography in nonalcoholic fatty liver disease

IntroductionTwo-dimensional shear wave elastography (2D-SWE) and vibration-controlled transient elastography (VCTE) provide noninvasive assessment of hepatic fibrosis. We compared performance of 2D-SWE and VCTE for fibrosis detection in nonalcoholic fatty liver disease (NAFLD).MethodsWe performed a prospective study of adults with NAFLD who underwent 2D-SWE, VCTE, and liver biopsy analysis (using Nonalcoholic Steatohepatitis Clinical Research Network scoring system). The primary outcome was hepatic fibrosis (stage ⩾ 1); secondary outcomes included dichotomized fibrosis stages. Area under receiver operating characteristic curve (AUROC) analyses were used to compare 2D-SWE and VCTE performance.ResultsA total of 114 adults with a median BMI of 31.2 kg/m2 were included. The VCTE was better than 2D-SWE for the detection of fibrosis (AUROC: 0.81 versus 0.72, p = 0.03). The VCTE detected fibrosis stage 2, 3, or 4 with AUROCs of 0.86 (95% CI, 0.80-0.93), 0.91 (95% CI, 0.82-0.99), and 0.96 (95% CI, 0.91-1.00). The 2D-SWE detected fibrosis stage 2, 3, or 4 with AUROCs of 0.84 (95% CI, 0.76-0.92), 0.88 (95% CI, 0.81-0.96), and 0.93 (95% CI, 0.86-0.99).ConclusionIn a prospective study including more than 100 adults with NAFLD, we found VCTE to be more accurate than 2D-SWE in detecting fibrosis; these modalities, however, are comparable in assessing for higher stages of fibrosis

Gut metagenome-derived signature predicts hepatic decompensation and mortality in NAFLD-related cirrhosis.

BACKGROUND: There are limited data on the diagnostic accuracy of gut microbial signatures for predicting hepatic decompensation in patients with cirrhosis. AIMS: To determine whether a stool metagenome-derived signature accurately detects hepatic decompensation and mortality risk in cirrhosis secondary to non-alcoholic fatty liver disease (NAFLD) METHODS: Shotgun metagenomic sequencing was performed on faecal samples collected at study entry from a prospective cohort of adults with NAFLD-related cirrhosis. A Random Forest machine learning algorithm was utilised to identify a metagenomic signature of decompensated cirrhosis (defined by ascites, hepatic encephalopathy or variceal haemorrhage) and subsequently validated in an external cohort. A Cox proportional hazards regression model was used to examine predictors of all-cause mortality. RESULTS: In all, 25 adults with NAFLD-related cirrhosis (training cohort) were included. Among the 16 participants with decompensated cirrhosis, 33% had ascites, 56% had hepatic encephalopathy and 22% had experienced a variceal haemorrhage (not mutually exclusive). We identified a stool metagenomic signature comprising 13 discriminatory species that reliably distinguished decompensated NAFLD-related cirrhosis (diagnostic accuracy, 0.97, 95% confidence interval [CI] 0.96-0.99). Diagnostic accuracy of the 13-species signature remained high after adjustment for lactulose (area under the curve [AUC] 0.99) and rifaximin use (AUC 0.93). The discriminative ability of 13-species metagenomic signature was robust in an independent test cohort (AUC 0.95, 95% CI 0.81-1.00). The 13-species metagenomic signature (hazard ratio [HR] 1.54, 95% CI 1.10-2.15, p = 0.01) was a stronger predictor of mortality than the Model for End-Stage Liver Disease score (HR 1.25, 95% CI 1.03-1.53, p = 0.03). CONCLUSIONS: This study provides evidence for a gut metagenome-derived signature with high diagnostic accuracy for hepatic decompensation that predicts risk of mortality in NAFLD-related cirrhosis

A prospective study on the prevalence of NAFLD, advanced fibrosis, cirrhosis and hepatocellular carcinoma in people with type 2 diabetes

Background & aimsThere are limited prospective data on patients with type 2 diabetes mellitus (T2DM) specifically enrolled and systematically assessed for advanced fibrosis or cirrhosis due to non-alcoholic fatty liver disease (NAFLD). Therefore, we aimed to evaluate the prevalence of advanced fibrosis and cirrhosis in a prospectively recruited cohort of adults with T2DM.MethodsThis prospective study enrolled adults aged ≥50 years with T2DM, recruited from primary care or endocrinology clinics. Participants underwent a standardized clinical research visit with MRI-proton density fat fraction (MRI-PDFF), magnetic resonance elastography (MRE), vibration-controlled transient elastography (VCTE) and controlled-attenuation parameter. NAFLD was defined as MRI-PDFF ≥5% after exclusion of other liver diseases. Advanced fibrosis and cirrhosis were defined by established liver stiffness cut-off points on MRE or VCTE if MRE was not available.ResultsOf 524 patients screened, 501 adults (63% female) with T2DM met eligibility. The mean age and BMI were 64.6 (±8.1) years and 31.4 (±5.9) kg/m2, respectively. The prevalence of NAFLD, advanced fibrosis and cirrhosis was 65%, 14% and 6%, respectively. In multivariable adjusted models, adjusted for age and sex, obesity and insulin use were associated with increased odds of advanced fibrosis (odds ratio 2.50; 95% CI 1.38-4.54; p = 0.003 and odds ratio 2.71; 95% CI 1.33-5.50; p = 0.006, respectively). Among 29 patients with cirrhosis, two were found to have hepatocellular carcinoma and one patient had gallbladder adenocarcinoma.ConclusionUtilizing a uniquely well-phenotyped prospective cohort of patients aged ≥50 years with T2DM, we found that the prevalence of advanced fibrosis was 14% and that of cirrhosis was 6%. These data underscore the high risk of advanced fibrosis/cirrhosis in adults aged ≥50 years with T2DM.Impact and implicationsNon-alcoholic fatty liver disease (NAFLD) is common in patients with type 2 diabetes (T2DM), however, there are limited prospective data characterizing the prevalence of advanced fibrosis and cirrhosis using the most accurate non-invasive biomarkers of liver fat and fibrosis. We show that 14% of older adults with T2DM have advanced fibrosis and 6% have cirrhosis, which places them at risk for liver failure and liver cancer. Accurate prevalence rates and comparative analysis regarding the diagnostic accuracy of non-invasive tests in this population will guide the optimal screening strategy and future cost-effectiveness analyses. These results will inform future Hepatology and Endocrinology practice guidelines regarding NAFLD screening programs in older adults with T2DM

Liver stiffness by magnetic resonance elastography is associated with increased risk of cardiovascular disease in patients with non‐alcoholic fatty liver disease

BackgroundMagnetic resonance elastography (MRE) is a reliable non-invasive alternative to liver biopsy for assessing liver fibrosis. There are limited data regarding an association between liver fibrosis by MRE and risk of cardiovascular disease (CVD).AimTo investigate the association of high-risk CVD phenotype determined by coronary artery calcification (CAC) with liver fibrosis by MRE in patients with non-alcoholic fatty liver disease (NAFLD).MethodThis was a cross-sectional analysis of well-characterised, prospective cohorts including 105 patients with NAFLD (MR imaging-derived proton density fat fraction ≥ 5%) with contemporaneous cardiac computed tomography (CT) and MRE. Patients were assessed using MRE for liver stiffness, and cardiac CT for the presence of CAC (defined as coronary artery calcium score > 0). Odds of presence of CAC were analysed using logistic regression analysis.ResultsThe average age and body mass index were 54.9 years and 32.9 kg/m2 respectively. In this cohort, 49.5% of patients had CAC and 35.2% had significant liver fibrosis (defined as MRE ≥2.97 kPa). Compared to patients without CAC, those with CAC were older (50.0 [39.0-59.0] vs 63.0 [55.5-67.5], P < 0.001) and had higher Framingham risk score (FRS, 1.0 [0.5-3.5] vs 6.0 [2.0-12.0], P < 0.001). In multivariable-adjusted analysis, liver stiffness as a continuous trait on MRE was independently associated with the presence of CAC in a sex and age-adjusted model (adjusted odd ratios [aOR] = 2.23, 95% confidence interval [CI] = 1.31-4.34, P = 0.007) as well as in a FRS-adjusted model (aOR = 2.16, 95% CI = 1.29-4.09, P = 0.008). When analysed as a dichotomous trait, significant fibrosis (MRE-stiffness ≥2.97 kPa) remained independently associated with the presence of CAC in both FRS-adjusted model and sex and age-adjusted model (aOR = 3.21-3.53, P = 0.013-0.017). In addition, CAC was more prevalent in patients with significant fibrosis than those without as determined by MRE (67.6% vs 39.7%, P = 0.012).ConclusionLiver stiffness determined by MRE is an independent predictor for the presence of CAC in patients with NAFLD. Patients with NAFLD and significant fibrosis by MRE should be considered for further cardiovascular risk assessment, regardless of their FRS

Direct Comparison of Quantitative US versus Controlled Attenuation Parameter for Liver Fat Assessment Using MRI Proton Density Fat Fraction as the Reference Standard in Patients Suspected of Having NAFLD.

Background MRI-derived proton density fat fraction (PDFF) is an accurate, reliable, and safe biologic marker for use in the noninvasive diagnosis of hepatic steatosis in patients with nonalcoholic fatty liver disease (NAFLD). Because of the cost and limited availability of MRI, it is necessary to develop an accurate method to diagnose NAFLD with potential point-of-care access. Purpose To compare the diagnostic accuracy of the quantitative US (QUS) fat fraction (FF) estimator with that of the controlled attenuation parameter (CAP) in the diagnosis of NAFLD using contemporaneous MRI-derived PDFF as the reference standard. Materials and Methods Participants with or suspected of having NAFLD were prospectively recruited at the NAFLD Research Center between July 2015 and July 2019. All participants underwent MRI-derived PDFF measurement, transient elastography with CAP measurement, and QUS. QUS FF was derived using computed QUS parameters from the acquired radiofrequency US data using a calibrated reference phantom. The area under the receiver operating characteristic curve (AUC) was calculated to assess the accuracy of QUS FF and CAP in the diagnosis of hepatic steatosis (defined as MRI-derived PDFF ≥ 5%). AUCs were compared using the DeLong test. Results A total of 123 participants were included (mean age, 52 years ± 13 [SD]; 67 [54%] women). Of these participants, 100 (81%) had MRI-derived PDFF of 5% or more. QUS FF had a significantly higher AUC for diagnosis of NAFLD than did CAP (0.92 [95% CI: 0.87, 0.98] vs 0.79 [95% CI: 0.67, 0.90], P = .03). QUS FF had a sensitivity of 98% (98 of 100) and a specificity of 48% (11 of 23). CAP had a sensitivity of 87% (87 of 100) and a specificity of 57% (13 of 23). Conclusion The quantitative US fat fraction estimator is more accurate than the controlled attenuation parameter in the diagnosis of hepatic steatosis in patients with or suspected of having nonalcoholic fatty liver disease. © RSNA, 2022 Online supplemental material is available for this article. See also the editorial by Ito in this issue

MRE combined with FIB-4 (MEFIB) index in detection of candidates for pharmacological treatment of NASH-related fibrosis

ObjectivePatients with non-alcoholic fatty liver disease (NAFLD) with ≥stage 2 fibrosis are at increased risk for liver-related mortality and are candidates for pharmacological therapies for treatment of NAFLD. The aim of this prospective cohort study is to examine the diagnostic accuracy of MR elastography (MRE) combined with fibrosis-4 (FIB-4) in diagnosing ≥stage 2 fibrosis (candidates for pharmacological therapies).DesignThis is a cross-sectional analysis of a prospective cohort (University of California at San Diego (UCSD)-NAFLD) including 238 consecutive patients with contemporaneous MRE and biopsy-proven NAFLD. Non-alcoholic steatohepatitis-Clinical Research Network-Histologic Scoring System was used to assess histology. The radiologist and pathologist were blinded to clinical, pathological and imaging data, respectively. Receiver operating characteristics (ROCs) were determined to examine the diagnostic accuracy of MRE and FIB-4 for diagnosis of ≥stage 2 fibrosis in NAFLD. We then validated these findings in an independent validation cohort derived from Yokohama City University in Japan (Japan-NAFLD Cohort; N=222 patients).ResultsIn the UCSD-NAFLD (training) Cohort, MRE demonstrated a clinically significant diagnostic accuracy for the detection of ≥stage 2 fibrosis with an area under the ROC curve (AUROC) of 0.93 (95% CI 0.90 to 0.97) vs FIB-4 with an AUROC of 0.78 (95% CI 0.71 to 0.85), which was both clinically and statistically significant (p<0.0001). We then combined MRE with FIB-4 (MRE ≥3.3 kPa and FIB-4 ≥1.6) to develop a clinical prediction rule to rule in ≥stage 2 fibrosis patients which had positive predictive value (PPV) of 97.1% (p<0.02) in the UCSD-NAFLD cohort (AUROC of 0.90 (95% CI 0.85 to 0.95)) which remained significant at PPV of 91.0% (p<0.003) in the Japan-NAFLD Cohort (AUROC of 0.84 (95% CI 0.78 to 0.89)).ConclusionMRE combined with FIB-4 (MEFIB) index may be used for non-invasive identification of candidates for (≥stage 2 fibrosis) pharmacological therapy among patients with NAFLD with a high PPV