Opportunities for organoids as new models of aging.

The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (AML), we demonstrated that genetically distinct AML subtypes display diametrically opposed DNA methylation patterns. As compared to normal controls, we observed widespread hypermethylation in IDH mutant AMLs, preferentially targeting promoter regions and CpG islands neighboring the transcription start sites of genes. In contrast, AMLs harboring translocations affecting the MLL gene displayed extensive loss of methylation of an almost mutually exclusive set of CpGs, which instead affected introns and distal intergenic CpG islands and shores. When analyzed in conjunction with gene expression profiles, it became apparent that these specific patterns of DNA methylation result in differing roles in gene expression regulation. However, despite this subtype-specific DNA methylation patterning, a much smaller set of CpG sites are consistently affected in both AML subtypes. Most CpG sites in this common core of aberrantly methylated CpGs were hypermethylated in both AML subtypes. Therefore, aberrant DNA methylation patterns in AML do not occur in a stereotypical manner but rather are highly specific and associated with specific driving genetic lesions

Intraoperative Hypertension and Thrombocytopenia Associated With Intracranial Hemorrhage After Liver Transplantation.

BackgroundIntracranial hemorrhage (ICH) is a devastating complication. Although hypertension and thrombocytopenia are well-known risk factors for ICH in the general population, their roles in ICH after liver transplantation (LT) have not been well established.MethodsWe performed a retrospective study and hypothesized that intraoperative hypertension and thrombocytopenia were associated with posttransplant ICH. New onset of spontaneous hemorrhage in the central nervous system within 30 days after LT were identified by reviewing radiologic reports and medical records. Risk factors were identified by multivariate logistic regression. Receiver operating characteristic analysis and Youden index were used to find the cutoff value with optimal sensitivity and specificity.ResultsOf 1836 adult patients undergoing LT at University of California, Los Angeles, 36 (2.0%) developed ICH within 30 days after LT. Multivariate logistic regression demonstrated that intraoperative mean arterial pressure ≥105 mm Hg (≥10 min) (odds ratio, 6.5; 95% confidence interval, 2.7-7.7; P < 0.001) and platelet counts ≤30 × 10/L (odds ratio, 3.3; 95% confidence interval, 14-7.7; P = 0.006) were associated with increased risk of postoperative ICH. Preoperative total bilirubin ≥7 mg/dL was also a risk factor. Thirty-day mortality in ICH patients was 48.3%, significantly higher compared with the non-ICH group (3.0%; P < 0.001). Patients with all 3 risk factors had a 16% chance of developing ICH.ConclusionsIn the current study, postoperative ICH was uncommon but associated with high mortality. Prolonged intraoperative hypertension and severe thrombocytopenia were associated with postoperative ICH. More studies are warranted to confirm our findings and develop a strategy to prevent this devastating posttransplant complication

Development of a disease-specific questionnaire to measure health-related quality of life in liver transplant recipients.

Currently, no disease-targeted instrument is available for measuring health-related quality of life (HRQOL) in liver transplant recipients. We developed and tested a post-liver transplant quality of life (pLTQ) instrument. Item selection for the pLTQ instrument was based on responses from liver transplant recipients, 12 liver experts, and a literature search. Impact scores were generated, and a factor analysis was conducted to organize the items into domains. Questions were constructed for each item, and redundant questions were removed. The pLTQ instrument was initially administered to 196 liver transplant patients and then was again administered to 77 patients 6 to 9 months later with a generic HRQOL survey [Medical Outcomes Study Short Form 36 (SF-36)]. Analysis of variance was used to compare the scores of patients at different times since transplantation and with various indications for transplantation. After redundancies were eliminated, the pLTQ instrument included 32 items in 8 domains: Emotional Function, Worry, Medications, Physical Function, Healthcare, Graft Rejection Concern, Financial, and Pain. We found stable pLTQ instrument and SF-36 instrument scores over time. Data 6 to 9 months after the initial assessment indicated stable quality of life outcomes. The pLTQ instrument is applicable to a variety of liver transplant recipients. The questionnaire was tested with a cross-sectional and longitudinal approach

Development of a disease-specific questionnaire to measure health-related quality of life in liver transplant recipients.

Currently, no disease-targeted instrument is available for measuring health-related quality of life (HRQOL) in liver transplant recipients. We developed and tested a post-liver transplant quality of life (pLTQ) instrument. Item selection for the pLTQ instrument was based on responses from liver transplant recipients, 12 liver experts, and a literature search. Impact scores were generated, and a factor analysis was conducted to organize the items into domains. Questions were constructed for each item, and redundant questions were removed. The pLTQ instrument was initially administered to 196 liver transplant patients and then was again administered to 77 patients 6 to 9 months later with a generic HRQOL survey [Medical Outcomes Study Short Form 36 (SF-36)]. Analysis of variance was used to compare the scores of patients at different times since transplantation and with various indications for transplantation. After redundancies were eliminated, the pLTQ instrument included 32 items in 8 domains: Emotional Function, Worry, Medications, Physical Function, Healthcare, Graft Rejection Concern, Financial, and Pain. We found stable pLTQ instrument and SF-36 instrument scores over time. Data 6 to 9 months after the initial assessment indicated stable quality of life outcomes. The pLTQ instrument is applicable to a variety of liver transplant recipients. The questionnaire was tested with a cross-sectional and longitudinal approach

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia

Here we used Illumina NGS for high-throughput profiling of the DNA methylome in two human colon cancer derived cell lines, two human normal bone marrow CD34+ controls and in five human Acutre Myeloid Leukeima patient samples. These data can be used to determine the CpG cytosine methylation pattern at base pair resolution in each sample and to determine differentially methylated cytosines and regions between samples Reduced Representation Bisulfite Sequencing (RRBS) and Extended Reduced Representation Bisulfite Sequencing (ERRBS) on genomic DNA. We used colon cancer cell lines (two) to establish reproducbility and range of assay sensitivity. We used Acute Myeloid Leukemia patient samples and CD34+ bone marrow cells as controls to determine the methylome pattern in the patient sample

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia

Here we used Illumina NGS for high-throughput profiling of the DNA methylome in two human colon cancer derived cell lines, two human normal bone marrow CD34+ controls and in five human Acutre Myeloid Leukeima patient samples. These data can be used to determine the CpG cytosine methylation pattern at base pair resolution in each sample and to determine differentially methylated cytosines and regions between samples Reduced Representation Bisulfite Sequencing (RRBS) and Extended Reduced Representation Bisulfite Sequencing (ERRBS) on genomic DNA. We used colon cancer cell lines (two) to establish reproducbility and range of assay sensitivity. We used Acute Myeloid Leukemia patient samples and CD34+ bone marrow cells as controls to determine the methylome pattern in the patient sample

Multi-Center Analysis of Liver Transplantation for Combined Hepatocellular Carcinoma-Cholangiocarcinoma Liver Tumors.

BACKGROUND: Combined hepatocellular-cholangiocarcinoma liver tumors (cHCC-CCA) with pathologic differentiation of both hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma within the same tumor are not traditionally considered for liver transplantation due to perceived poor outcomes. Published results are from small cohorts and single centers. Through a multi-center collaboration, we performed the largest analysis to date of the utility of liver transplantation for cHCC-CCA. STUDY DESIGN: Liver transplant and resection outcomes for HCC (n=2998) and cHCC-CCA (n=208) were compared in a 12-center retrospective review (2009-2017). Pathology defined tumor type. Tumor burden was based on radiologic Milan criteria at time of diagnosis and applied to cHCC-CCA for uniform analysis. Kaplan-Meier survival curves and log-rank test were used to determine overall survival and disease-free survival. Cox regression was used for multivariate survival analysis. RESULTS: Liver transplant for cHCC-CCA (n=67) and HCC (n=1814) within Milan had no significant difference in overall survival (5-yr cHCC-CCA 70.1%, HCC 73.4%, p=0.806) despite higher cHCC-CCA recurrence rates (23.1% vs 11.5% 5-years, p CONCLUSIONS: Regardless of tumor burden, outcomes following liver transplant are superior to resection for patients with cHCC-CCA. Within Milan criteria, liver transplant for cHCC-CCA and HCC results in similar overall survival justifying consideration of transplantation due to the higher chance of cure with liver transplantation in this traditionally excluded population

Posttransplant Outcomes in Older Patients With Hepatocellular Carcinoma Are Driven by Non–Hepatocellular Carcinoma Factors

The incidence of hepatocellular carcinoma (HCC) is growing in the United States, especially among the elderly. Older patients are increasingly receiving transplants as a result of HCC, but the impact of advancing age on long-term posttransplant outcomes is not clear. To study this, we used data from the US Multicenter HCC Transplant Consortium of 4980 patients. We divided the patients into 4 groups by age at transplantation: 18 to 64 years (n = 4001), 65 to 69 years (n = 683), 70 to 74 years (n = 252), and ≥75 years (n = 44). There were no differences in HCC tumor stage, type of bridging locoregional therapy, or explant residual tumor between the groups. Older age was confirmed to be an independent and significant predictor of overall survival even after adjusting for demographic, etiologic, and cancer-related factors on multivariable analysis. A dose-response effect of age on survival was observed, with every 5-year increase in age older than 50 years resulting in an absolute increase of 8.3% in the mortality rate. Competing risk analysis revealed that older patients experienced higher rates of non-HCC-related mortality (P = 0.004), and not HCC-related death (P = 0.24). To delineate the precise cause of death, we further analyzed a single-center cohort of patients who received a transplant as a result of HCC (n = 302). Patients older than 65 years had a higher incidence of de novo cancer (18.1% versus 7.6%; P = 0.006) after transplantation and higher overall cancer-related mortality (14.3% versus 6.6%; P = 0.03). Even carefully selected elderly patients with HCC have significantly worse posttransplant survival rates, which are mostly driven by non-HCC-related causes. Minimizing immunosuppression and closer surveillance for de novo cancers can potentially improve the outcomes in elderly patients who received a transplant as a result of HCC

DNA methylation and gene expression relationships display subtype-specific differences.

<p>CpG islands and shores across the genome were categorized into those located upstream from a transcription start site (TSS), overlapping a TSS or located downstream from a TSS. Boxplots are plotted that illustrate the maximum DNA methylation levels at CpGs within these CpG islands and CpG shores for the top 15th percentile expressed genes (right) and the bottom 15th percentile expressed genes (left). Each row shows a representative sample for each type: Normal bone marrow (top); IDH-mut AML (middle) and MLLr AML (bottom). In all sample types CpG islands overlapping a TSS displayed lower methylation levels in highly expressed genes and higher methylation levels in genes that were expressed at low levels. In MLLr AMLs this relationship between expression and methylation levels further extended into CpG shores, and was also observed at CpG islands and shores upstream and downstream from the TSS. IDH-mut AMLs, and to a lesser degree NBM samples, displayed higher methylation levels at CpG shores of genes with high expression levels, while low methylation levels were observed at these shores for genes expressed at low levels.</p