Turnover Profiles Research Articles

7 Flexible probabilistic methods to unlock the clinical potential of liquid biopsy sampling

OBJECTIVES/GOALS: Decoding the origins of cell-free DNA (cfDNA) released from dying cells in a liquid biopsy sample (e.g. blood) offers the potential to provide insight into the dynamic, organism-wide changes reflective of health and disease. Thus, making cfDNA an ideal target for serial, minimally invasive monitoring of disease-related changes. METHODS/STUDY POPULATION: We develop a probabilistic method that leverages the co-regulation of neighboring CpG sites on individual methylome-wide sequencing (WGBS) reads to more flexibly model cell-specific methylation compared to prior methods that focus on the methylation rate of a single CpG site. We then extend our cross-sectional model to account for sequential sampling within the same subject. The increased sampling frequency is critical to identifying the evolutionary dynamics of disease progression influencing treatment response and resistance, and disease recurrence. We utilize Bayesian inference techniques to model patient-specific longitudinal profiles of cell-type turnover in simulated serial samples. RESULTS/ANTICIPATED RESULTS: We found our model more effective at capturing a range of methylation patterns on cfDNA fragments with lower Root Mean Square Error across simulations compared to a single CpG model. We apply our model to detect significant (p < 0.05, Friedman’s test) increases in cellular contributions from lung and cardiac tissue in breast cancer patients (n=15) undergoing radiation therapy compared to baseline. We also identify signals of radiation induced toxicity to the liver in right-sided breast cancer patients (n=8) receiving radiation treatment compared to left-sided breast cancer patients (n=7). Finally, we show our extended model results in more efficient estimates of simulated cell-type turnover profiles compared to analyzing serial samples cross-sectionally, ignoring the longitudinal nature of the data. DISCUSSION/SIGNIFICANCE: Here we address an unmet need in developing novel statistical methodologies to decode the origins of methylated cfDNA obtained from liquid biopsy samples. We demonstrate the far-ranging clinical utility of serial liquid biopsy sampling to complement and advance the standards of clinical care in oncology and other pathologies.

In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development

Protein translational control is critical for ensuring that the fetus develops correctly and that necessary organsand tissues are formed and functional. We developed an in utero method to quantify tissue-specific protein dynamics by monitoring amino acid incorporation into the proteome after pulse injection. Fetuses of pregnant mice were injected with isotopically labeled lysine and arginine via the vitelline vein at various embyonic days, and organs and tissues were harvested. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates were calculated between 3.81E-5 and 0.424 h-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver vs. brain); however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates, which correlated with known physiological changes during mouse development.

Post‐translational modification and phenotype

Post‐translational modification and phenotype

Effect of α-helical domain of Gi/o α subunit on GDP/GTP turnover.

Heterotrimeric guanine nucleotide-binding proteins (G proteins) are composed of α, β, and γ subunits, and Gα has a GDP/GTP-binding pocket. When a guanine nucleotide exchange factor (GEF) interacts with Gα, GDP is released, and GTP interacts to Gα. The GTP-bound activated Gα dissociates from GEF and Gβγ, mediating the induction of various intracellular signaling pathways. Depending on the sequence similarity and cellular function, Gα subunits are subcategorized into four subfamilies: Gαi/o, Gαs, Gαq/11, and Gα12/13. Although the Gαi/o subtype family proteins, Gαi3 and GαoA, share similar sequences and functions, they differ in their GDP/GTP turnover profiles, with GαoA possessing faster rates than Gαi3. The structural factors responsible for these differences remain unknown. In this study, we employed hydrogen/deuterium exchange mass spectrometry and mutational studies to investigate the factors responsible for these functional differences. The Gα subunit consists of a Ras-like domain (RD) and an α-helical domain (AHD). The RD has GTPase activity and receptor-binding and effector-binding regions; however, the function of the AHD has not yet been extensively studied. In this study, the chimeric construct containing the RD of Gαi3 and the AHD of GαoA showed a GDP/GTP turnover profile similar to that of GαoA, suggesting that the AHD is the major regulator of the GDP/GTP turnover profile. Additionally, site-directed mutagenesis revealed the importance of the N-terminal part of αA and αA/αB loops in the AHD for the GDP/GTP exchange. These results suggest that the AHD regulates the nucleotide exchange rate within the Gα subfamily.

Dual current anomalies and quantum transport within extended reservoir simulations

Quantum transport simulations are rapidly evolving and now encompass well-controlled tensor network techniques for many-body limits. One powerful approach combines matrix product states with extended reservoirs. In this method, continuous reservoirs are represented by explicit, discretized counterparts and a chemical potential or temperature drop is maintained by external relaxation. Currents are strongly influenced by relaxation when it is very weak or strong, resulting in a simulation analog of Kramers' turnover for solution-phase chemical reactions. At intermediate relaxation, the intrinsic conductance, that given by the Landauer or Meir-Wingreen expressions, moderates the current. We demonstrate that strong impurity scattering (i.e., a small steady-state current) reveals anomalous transport regimes within this methodology at weak-to-moderate and moderate-to-strong relaxation. The former is due to virtual transitions and the latter to unphysical broadening of the populated density of states. Thus, the turnover analog has $five$ standard transport regimes, further constraining the parameters that lead to recovery of the intrinsic conductance. In the worst case, the common strategy of choosing a relaxation strength proportional to the reservoir level spacing can prevent convergence to the continuum limit. This advocates a simulation strategy where one utilizes the current versus relaxation turnover profiles to identify simulation parameters that most efficiently reproduce the intrinsic physical behavior.

Non-compete Agreements, Wages and Efficiency: Theory and Evidence from Brazilian Football

We propose a model to study non-compete agreements and evaluate their quantitative effects. We explore an exogenous policy change that removed non-compete clauses in the market for Brazilian footballers, the Pele Act of 1998. The Act raised players' lifetime income but changed the wage profile in a heterogeneous way, reducing young players' salaries. We structurally estimate the model's parameters by matching wages and turnover profiles in the post Act period. By changing a single parameter related to the non-compete friction, we can match the changes in the age-earnings profile. We then show that the bulk of income gains is due to distributional forces, with efficiency gains playing a minor role.

402 Awardee Talk - Efficiency of nutrient use in ruminants: Current understanding and emerging questions

Abstract Because feed costs represent a large proportion of total costs for ruminant production systems, improving the efficiency of nutrient utilization is an important goal for improving profitability and sustainability. Research on nutrient utilization in ruminants dates back to the 1800s when the first nutrient balance experiments were conducted. The concept of efficiency is complex and can be expressed in many ways. Different approaches should be used when examining economic efficiency vs. biological efficiency, growing vs. mature animals, or answering research questions vs. use in a production setting. Additionally, animal efficiency can be examined at different scales of complexity including animal, tissue, cell, or molecular levels, and at the level of total feed, feedstuff, or specific nutrient. Some of the facets that have been shown to be associated with animal efficiency include body composition, feed intake and digestion, heat production, blood metabolites and hormones, tissue mass, cell proliferation, protein turnover, ion transport, mitochondrial function, mRNA or protein expression profiles, and genomic polymorphisms within the animal, and composition and diversity of the gastrointestinal microbiome. Large amounts of information are being generated at the genomic, transcriptomic, and proteomic levels which will add to our knowledge about what factors are associated with animal efficiency. Nutrients, such as amino acids, play an important role to meet requirements for maintenance and production and have many other physiological functions regulating metabolism in the animal. There is potential to develop nutrient supplementation, or feeding, strategies to alter metabolism and improve nutrient utilization. Future research is needed to better define the mechanisms influencing efficiency of utilization of individual nutrients, rather than feed dry matter, and to develop management, nutritional, or animal breeding approaches to improve animal efficiency through altering whole animal, tissue, cellular, and molecular facets known to be associated with differences in animal efficiency.

Collagen turnover profiles in chronic kidney disease

Renal fibrosis is a hallmark of chronic kidney disease (CKD) caused by an imbalance between formation and degradation of extracellular matrix proteins. We investigated the collagen turnover profile of 81 non-dialysis CKD stage 2–5 patients by measuring peptides reflecting formation and degradation of collagen type (COL) I, III, IV, and VI. Based on the collagen turnover profile, we identified four clusters of patients. Cluster 1 contained one patient with prostate cancer, who had a distinct collagen turnover. The other clusters generally had severe (Cluster 2), moderate (Cluster 4), or mild CKD (Cluster 3). Cluster 4 patients were characterized by higher levels of COL III, COL IV, and COL VI (all p < 0.001) degradation fragments in plasma, while patients in Clusters 2 and 4 had higher levels of COL VI formation (p < 0.05). COL IV fragments in plasma were lower in Cluster 2 (p < 0.01). Urinary COL III fragments decreased from Cluster 3 to 4, and from Cluster 4 to 2 (both p < 0.001). We show that patients with similar kidney function have a different collagen remodeling profile, suggesting that different phenotypes exist with different disease activity and potentially disease progression. Biomarkers of collagen remodeling could provide additional information to traditional markers of renal function.

Energy profiling of dairy cows from routine milk mid-infrared analysis

The balance of body energy within and across lactations can have health and fertility consequences for the dairy cow. This study aimed to create a large calibration data set of dairy cow body energy traits across the cow's productive life, with concurrent milk mid-infrared (MIR) spectral data, to generate a prediction tool for use in commercial dairy herds. Detailed phenotypic data from 1,101 Holstein Friesian cows from the Langhill research herd (SRUC, Scotland) were used to generate energy balance (EB) and effective energy intake (EI), both in megajoules per day. Pretreatment of spectral data involved standardization to account for drift over time and machine. Body energy estimates were aligned with their spectral data to generate a prediction of these traits based on milk MIR spectroscopy. After data edits, partial least squares analysis generated prediction equations with a coefficient of determination from split sample 10-fold cross validation of 0.77 and 0.75 for EB and EI, respectively. These prediction equations were applied to national milk MIR spectra on over 11 million animal test dates (January 2013 to December 2016) from 4,453 farms. The predictions generated from these were subject to phenotypic analyses with a fixed regression model highlighting differences between the main dairy breeds in terms of energy traits. Genetic analyses generated heritability estimates for EB and EI ranging from 0.12 to 0.17 and 0.13 to 0.15, respectively. This study shows that MIR-based predictions from routinely collected national data can be used to generate predictions of dairy cow energy turnover profiles for both animal management and genetic improvement of such difficult and expensive-to-record traits.

Multi-omic measurements of heterogeneity in HeLa cells across laboratories.

Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.

Identification and Characterization of Canine Ligament Progenitor Cells and Their Extracellular Matrix Niche.

Ligaments are prone to injury and degeneration in humans and animals, however the healing potential of ligament is poor and current treatment options ineffective. Stem cell-based therapies hold potential for treatment of ligament injuries. This study aimed to characterize a ligament progenitor cell (LPC) population and to identify specific niche components which could promote the survival and function of LPCs. LPCs were isolated from canine cranial cruciate ligament and characterized for clonogenicity, multipotency and marker expression. The extracellular matrix (ECM) composition was characterized by the novel application of a metabolic labeling and mass spectrometry technique. LPCs demonstrated clonogenicity, multipotency, and stem cell marker expression. A number of different collagens, glycoproteins, and proteoglycans were identified in the LPC niche using proteomics. Metabolic labeling of cells demonstrated unique turnover profiles for distinct ECM protein groups, indicating the importance of certain niche components for LPC survival and function. The newly synthesized niche components identified in this study could be exploited to aid identification of LPCs and to promote their survival and function for potential ligament repair strategies.

Cross-species comparison of the metabolism and excretion of selexipag

1. The metabolism of the prostacyclin receptor agonist selexipag (NS-304; ACT-293987) and its active metabolite MRE-269 (ACT-333679) has been investigated in liver microsomes and hepatocytes of rats, dogs, and monkeys. MRE-269 formation is the main pathway of selexipag metabolism, irrespective of species. Some interspecies differences were evident for both compounds in terms of both metabolic turnover and metabolic profiles. The metabolism of MRE-269 was slower than that of selexipag in all three species.2. The metabolism of selexipag was also studied in bile-duct-cannulated rats and dogs after a single oral and intravenous dose of [14C]selexipag. MRE-269 acyl glucuronide was found in both rat and dog bile. Internal acyl migration reactions of MRE-269 glucuronide were identified in an experiment with the synthetic standard MRE-6001.3. MRE-269 was the major component in the faeces of rats and dogs. In ex vivo study using rat and dog faeces, selexipag hydrolysis to MRE-269 by the intestinal microflora is considered to be a contributory factor in rats and dogs.4. A taurine conjugate of MRE-269 was identified in rat bile sample. Overall, selexipag was eliminated via multiple routes in animals, including hydrolysis, oxidative metabolism, conjugation, intestinal deconjugation, and gut flora metabolism.

A hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells

Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3.3 and monitored the rate of H3.3 incorporation by ChIP-seq at varying time points following Dox induction, before and after RA-induced differentiation. Comparing H3.3 turnover profiles in ESCs and RA-treated cells, we identified a hyperdynamic H3.3-containing nucleosome at the −1 position in promoters of genes expressed in ESCs. This dynamic nucleosome is restricted and shifted downstream into the +1 position following differentiation. We suggest that histone turnover dynamics provides an additional mechanism involved in expression regulation, and that a hyperdynamic −1 nucleosome marks promoters in ESCs. Our data provide evidence for regional regulation of H3.3 turnover in ESC promoters, and calls for testing, in high resolution, the dynamic behavior of additional histone variants and other structural chromatin proteins.

H3.3 turnover: A mechanism to poise chromatin for transcription, or a response to open chromatin?

Histone H3.3 turnover displays distinct dynamics at various genomic elements such as promoters, enhancers, gene bodies, and heterochromatic regions, suggesting that it is differentially regulated according to chromatin context. Incorporation of variant histones into chromatin provides a mechanism to modulate chromatin states in addition to histone modifications. The replication-independent deposition and replacement of histone variant H3.3, i.e. H3.3 turnover, is mainly associated with transcriptional activity. H3.3 or H3.3-like histone turnover has been studied in various organisms from yeast to mammals. Here, we review the recent progress on this topic. The diversified turnover profiles of H3.3, and their corresponding underlying mechanisms, may reflect distinct requirements for chromatin accessibility in different biological events.

Leucine metabolism is not altered with improved insulin sensitivity following a 6‐month exercise program in pre‐diabetics (LB447)

Obesity is associated with decreased insulin sensitivity (IS), elevated plasma levels of branched‐chain amino acids (BCAAs), and accumulation of medium to long even‐chain acylcarnitines (AC; products of β‐oxidation). The purpose of this study was to investigate the relationship between BCAA metabolism and IS in overweight individuals. Whole‐body leucine turnover, IS and metabolic profiles were assessed from blood, muscle and breath samples at baseline in 10 healthy controls (CTRL: 5M, 5F; age 50 ± 3) and 9 overweight pre‐diabetic individuals (PD‐Pre: 5M, 4F; age 51 ± 2) using stable isotope tracers, hyperinsulinemic euglycemic clamp and metabolomics methods, respectively. PD then underwent a 6 month aerobic + resistance exercise program and repeated tests (PD‐Post). IS was higher in CTRL vs PD‐Pre, increased in PD‐Post, but remained lower than CTRL. Relative to lean mass, leucine breakdown, oxidation and synthesis were higher in PD‐Pre and PD‐Post vs CTRL, with no effect of exercise. Plasma leucine and valine were elevated in PD‐Pre vs CTRL and were not altered with exercise, while glycine was decreased in PD‐Pre vs CTRL, and increased in PD‐Post. Muscle AC were globally elevated in PD‐Pre vs CTRL and decreased in PD‐Post. We conclude exercise‐induced improvements in IS occur independent of changes in BCAA levels or metabolism, but are linked to decreased muscle AC levels, consistent with improved mitochondrial efficiency.Grant Funding Source: Supported by CV and Metabolic, a Pfizer research unit and NIH grant P01‐DK58398

Greater Skeletal Gains in Ovary Intact Rats at Maturity Are Achieved by Supplementing a Standardized Extract ofButea monospermaStem Bark that Confers Better Bone Conserving Effect following Ovariectomy and Concurrent Treatment Withdrawal

With a longitudinally designed study, we tested whether an acetone soluble fraction (ASF) from the stem bark of Butea monosperma resulted in maximizing bone gain in rats during growth and maturation and thus protected against osteopenia following ovariectomy (OVx) with concomitant treatment withdrawal. Female rats at weaning were given ASF (100 mg/kg/d) or vehicle for 12 weeks, and baseline skeletal parameters (micro-CT) and total plasma antioxidant status (TAS) were measured. At this stage, one group was OVx and the other group was sham operated. Vehicle group (untreated) after OVx was given E2 or continued with vehicle (OVx control). ASF group after OVx was given vehicle (ASF withdrawn, ASFW). After another 12 weeks, all groups were killed and various skeletal parameters were determined. ASF resulted in substantially better skeletal parameters and higher plasma TAS over control at maturity. Rats treated with ASF before OVx had reduced rates of bone loss compared to OVx control. Twelve weeks after OVx, the ASFW group exhibited better trabecular microarchitectural preservation, bone turnover profiles, increased cortical deposition, and biomechanical strength over the OVx control, and the effects were comparable to OVx + E2 group. ASF supplementation during skeletal growth could maximize bone accrual and could confer increased resistance to post-OVx osteopenia despite treatment withdrawal.

Tenure, Turnover, And Earnings Profiles In Germany And The United States

Employment tenure, job turnover and returns to general and specific skills are examined for male workers in Germany and the United States using data from the German Socio-Economic Panel and the Panel Study of Income Dynamics. Employment in Germany is characterized by longer duration and less frequent turnover than in the United States. Returns to experience and tenure are lower in Germany than in the U.S.; however, peak earnings occur later. This delayed peak in the employment-earnings profile provides an incentive for German workers to remain longer with their employers and change jobs less frequently.

Determination of Global Protein Turnover in Stressed Mycobacterium Cells Using Hybrid-Linear Ion Trap-Fourier Transform Mass Spectrometry

We determined the global protein turnover profiles for Mycobacterium smegmatis under acid shock and iron starvation conditions using a simple (15)N isotope doping technique and a complete medium replacement method for chasing. We used a high-resolution hybrid-linear ion trap-Fourier transform mass spectrometer coupled with nanoliquid chromatography separation to measure protein turnover values for 151 proteins over a dynamic range of 3 orders of magnitude ranging from about 0.2 to 500. Of these 151 proteins, 31 had significant protein turnover changes (p <0.05) at both stress conditions and had protein turnover values increased or decreased by more than 2-fold under at least one stress condition. Protein turnover increased under acid shock for 28 of the 31 proteins but decreased under iron starvation for all the 31 proteins. Only two proteins had protein turnover lowered by more than 2-fold (p <0.05) under both stress conditions, including an ATP synthase F1 beta subunit (MSMEG4921; AtpD) and a catalase/peroxidase (MSMEG6346; KatG). KatG is required for in vivo activation of isoniazid to be bacterialcidal. Decrease of KatG protein turnover under both stress conditions supports the view that isoniazid may induce a dormancy program in mycobacteria, which in turn limits the efficacy of this drug against dormant subpopulation of mycobacteria. Thus, measuring protein turnover in stressed Mycobacterium cells has implications in understanding drug action and resistance mechanisms.

Bone turnover markers in serum and periodontal microenvironments.

Periodontitis is characterized by altered bone turnover, but local measurements are difficult. The objective of this study was to develop a method to measure multiple markers of bone turnover from single samples collected at various bone surfaces of the periodontium, and to test the ratios of these markers against more traditional serum and gingival crevicular fluid (GCF) samples. Fourteen subjects with untreated periodontitis were recruited for sampling serum, GCF (from sites > or = 5 mm probing depth that bled on probing) and washes of periodontal bone surfaces (adjacent interproximal, vestibular cortical and trabecular bone) with a novel irrigating device. All samples were analyzed for osteocalcin (OC, bone turnover marker; RIA), cross-linked N-telopeptide of type I collagen (NTx, bone resorption marker; ELISA) and albumin (Alb, serum protein; ELISA). Results were reported as ratios: OC/NTx to determine relative bone turnover, and OC/Alb or NTx/Alb to determine local OC or NTx production. The OC/NTx ratio was significantly higher (p < or = 0.05) in serum vs. GCF (OC undetectable), interproximal bone and cortical vestibular bone, but significantly lower than in trabecular vestibular bone. The OC/Alb ratio for serum was also statistically lower than for vestibular trabecular bone. The NTx/Alb ratio for serum was statistically lower than for GCF and all the bone wash test sites. The results indicated considerable local production of both OC and NTx. This system demonstrated that multiple markers of bone turnover can be harvested by irrigation from periodontal bone microenvironments. Bone turnover profiles from periodontal bone surfaces and GCF differed from systemic bone turnover profiles (serum) and may be valuable in tracking site-specific responses to disease or treatment.

Molecular and kinetic features of transitional cell carcinomas of the bladder: biological and clinical implications.

Molecular and kinetic analyses have contributed to our understanding of the biology of transitional cell carcinomas (TCC) of the bladder. The concordant pattern of X-chromosome inactivation of multiple TCCs appearing at different times and at different sites and concordant genetic abnormalities in a subset of muscle-invasive TCC strongly support a monoclonal origin and a homogeneous tumor cell selection throughout the neoplasm. However, topographic intratumor heterogeneity results from the accumulation of genetic lesions in tumor suppressor genes, predominantly neurofibromatosis (NF)-1-defective in the superficial compartment and tumor protein p53 (TP53)-defective in the deep one, with lower proliferation and down-regulation of apoptosis in the latter. TCCs follow the general concept of multistep carcinogenesis and proceed through two distinct genetic pathways responsible for generating different TCC morphologies. These are the inactivation of cyclin-dependent kinase inhibitors (p15, p16, and p21WAF/CIP1) in low-grade TCC and early TP53-mediated abnormalities in high-grade TCC. TCC progression correlates with genetic instability and accumulation of collaborative genetic lesions mainly involving TP53, retinoblastoma (RB)-1, and growth factors. Distinctive genetic (low incidence of RB-1 and NF-1 abnormalities) and kinetic (slower cell turnover) profiles also correlate with a "single-file" infiltration pattern and poor survival in muscle-invasive TCCs. The underlying molecular changes of carcinoma in situ involve multiple and more extensive deletions (normally TP53-defective) than coexistent invasive TCC, suggesting an independent genetic evolution, while low-grade dysplasia is mainly polyclonal and shows a low rate of gene deletions.