scholarly journals Stochastic modelling reveals mechanisms of metabolic heterogeneity

2019 ◽  
Author(s):  
Mona K. Tonn ◽  
Philipp Thomas ◽  
Mauricio Barahona ◽  
Diego A. Oyarzún

Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and proteomic heterogeneity, yet it remains unclear if such variation permeates to the metabolic state of a cell. Here we propose a stochastic model to show that complex forms of metabolic heterogeneity emerge from fluctuations in enzyme expression and catalysis. The analysis predicts clonal populations to split into two or more metabolically distinct subpopulations. We reveal mechanisms not seen in deterministic models, in which enzymes with unimodal expression distributions lead to metabolites with a bimodal or multimodal distribution across the population. Based on published data, the results suggest that metabolite heterogeneity may be more pervasive than previously thought. Our work casts light on links between gene expression and metabolism, and provides a theory to probe the sources of metabolite heterogeneity.

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fang Wang ◽  
Qihan Wang ◽  
Vakul Mohanty ◽  
Shaoheng Liang ◽  
Jinzhuang Dou ◽  
...  

AbstractWe present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine named lineage speciation analysis (LSA), whichty facilitates discovery of fitness-associated alterations and genes from SCCN lineage trees. MEDALT appears more accurate than phylogenetics approaches in reconstructing copy number lineage. From data from 20 triple-negative breast cancer patients, our approaches effectively prioritize genes that are essential for breast cancer cell fitness and predict patient survival, including those implicating convergent evolution.The source code of our study is available at https://github.com/KChen-lab/MEDALT.


2017 ◽  
Vol 3 (1) ◽  
pp. 64-71 ◽  
Author(s):  
Prasanth Ganesan ◽  
Lalit Kumar

Background In the last decade, the use of imatinib has brought a paradigm shift in the management of chronic myeloid leukemia (CML). In India, imatinib has been available for more than a decade and has been made accessible to all segments of the population because of patient assistance programs and cheaper generic versions. Despite improvements in survival, there are unique challenges in the Indian context. Methods We reviewed published data pertaining to CML in India for the period of 1990 to 2016, using PubMed advanced search with the terms chronic myeloid leukemia and India, and included studies that reported on epidemiology, monitoring for therapy, treatment outcomes, and resistance. Additionally, the references in retrieved articles were also reviewed. Results Thirty-seven studies were identified. The incidence of CML may be slightly lower in India than in the West, but there was only a single article reporting population-based data. Indian patients presented with more advanced disease. Most centers have access to imatinib as first-line therapy, but there is limited availability of molecular monitoring and second-line therapy. Most of the outcome data were retrospective but seemed comparable with that reported in Western centers. Drug adherence was impaired in at least one third of patients and contributed to poor survival. Conclusion Focused prospective studies and cooperative studies might improve the quality of data available. Future studies should focus on adherence, its effects on outcomes, and methods to address this problem.


Author(s):  
Sarpreet S Sekhon ◽  
Katelynn Crick ◽  
Tyler W Myroniuk ◽  
Kevin S C Hamming ◽  
Mahua Ghosh ◽  
...  

Abstract Introduction Adrenal insufficiency (AI) is an uncommon, life-threatening disorder requiring lifelong treatment with steroid therapy and special attention to prevent adrenal crisis. Little is known about the prevalence of AI in Canada or healthcare utilization rates by these patients. Objective We aimed to assess the prevalence and healthcare burden of AI in Alberta, Canada. Methods This study used a population-based, retrospective administrative health data approach to identify patients with a diagnosis of AI over a 5-year period and evaluated emergency and outpatient healthcare utilization rates, steroid dispense records and visit reasons. Results The period prevalence of AI was 839 per million adults. Patients made an average of 2.3 and 17.8 visits per year in the emergency department and outpatient settings, respectively. This was 3-4 times as frequent as the average Albertan and only 5% were coded as visits for AI. The majority of patients were dispensed glucocorticoid medications only. Conclusion The prevalence of AI in Alberta is higher than published data in other locations. The frequency of visits suggests a significant healthcare burden and emphasizes the need for a strong understanding of this condition across all clinical settings. Our most concerning finding is that 94.3% of visits were not labelled with AI, even though many of the top presenting complaints were consistent with adrenal crisis. Several data limitations were discovered that suggest improvements in the standardization of data submission and coding can expand the yield of future studies using this method.


Author(s):  
Mona K. Tonn ◽  
Philipp Thomas ◽  
Mauricio Barahona ◽  
Diego A. Oyarzún

Metabolic heterogeneity is widely recognized as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular events. However, metabolism has been traditionally viewed as a purely deterministic process, on the basis that highly abundant metabolites tend to filter out stochastic phenomena. Here we bridge this gap with a general method for prediction of metabolite distributions across single cells. By exploiting the separation of time scales between enzyme expression and enzyme kinetics, our method produces estimates for metabolite distributions without the lengthy stochastic simulations that would be typically required for large metabolic models. The metabolite distributions take the form of Gaussian mixture models that are directly computable from single-cell expression data and standard deterministic models for metabolic pathways. The proposed mixture models provide a systematic method to predict the impact of biochemical parameters on metabolite distributions. Our method lays the groundwork for identifying the molecular processes that shape metabolic heterogeneity and its functional implications in disease.


2009 ◽  
Vol 15 (S1) ◽  
pp. 249-265 ◽  
Author(s):  
B. Browne ◽  
J. Duchassaing ◽  
F. Suter

ABSTRACTAll UK insurers exposed to longevity risk need to perform stress tests for their Individual Capital Assessment (ICA). Some have put in place deterministic models which are arguably too simple; others have developed stochastic models that can be demanding and complex.This paper presents a simple model to turn any deterministic mortality scenario into a stochastic model. We propose a simple model of stochastic variation that is easy to explain and to implement, which could be an alternative to and/or complete some of the well known models. The model can be applied to any best estimates of future mortality rates, as it aims to describe how longevity behaves around the projected expected values.The paper proposes a possible calibration on the England and Wales population mortality that produces a minimum indication of possible future variation and uses the results to validate the model's assumptions. Using sample portfolios and the stochastic model, we can simulate cash flows to determine the distribution of the net present values (NPV) of annuity outgo.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2727-2727
Author(s):  
Fredrik Ellin ◽  
Mats Jerkeman ◽  
Thomas Relander

Abstract Abstract 2727 T-cell lymphoblastic lymphoma (T-LBL) is a rare disease mainly affecting children and young adults. Commonly presenting with a large mass in the anterior mediastinum it represents the lymphoma end of the T-cell acute lymphoblastic leukemia (T-ALL) spectrum and as such has a high risk of CNS involvement. If present, cases with bone marrow infiltration < 25% are classified as T-LBL. The optimal standard treatment for adult T-LBL is not yet defined due to the rarity of the disorder and the consequent lack of randomized prospective trials. Hence, adults that are diagnosed with T-LBL are exposed to a range of chemotherapy regimens, according to a variety of local therapeutic guidelines. Most published data originates from clinical trials in the pediatric population. Here we present the treatment outcome and clinical prognostic factors from a population-based cohort of adult T-LBL patients. Using the Swedish Lymphoma Registry (SLR) all adult T-LBL patients diagnosed between January 2000 and December 2009 were identified in this study. Basic data was collected from the registry and further data was extracted from patient records after obtaining informed consent. Through the SLR 46 cases were identified. Seven cases were re-classified as T-ALL. Median age at diagnosis was 40 years (range 18–77 yrs) with a male:female ratio of 5:3. Bulky disease (>10cm) was present in 67%. Only 2 patients had CNS involvement at diagnosis while 18 (46%) presented with stage IV disease, 10 because of bone marrow involvement and 8 due to extensive extranodal disease. Median follow up for surviving patients was 6.5 years (range 2.0 – 11 yrs). The estimated 5-year OS was 42% for the entire cohort. Of 39 patients 1 declined participation, 1 died after the first cycle and 4 records could not be accessed, leaving 33 patients evaluable for treatment response. FDG-PET was performed in 13 patients after induction treatment. The ORR was 91% (33% CR, 58% PR, 9% SD). In many cases PR was due to PET negative residual masses. Thirty patients (age 18–66 yrs) received intensive ALL-like treatment. For this group treatments used were hyper-CVAD (n=19), LSA2L2 (n=4), VSTB -95 (n=2), NOPHO-ALL-HR (n=2), Euro LB -02 (n=1), GMALL 99/06 (n=1), ABCDV (n=1) resulting in an ORR of 97% (40% CR, 57% PR). No toxic death occurred. Consolidation consisted of radiation therapy against mediastinum followed by maintenance treatment in 3 patients, maintenance treatment in 19 patients, 2 underwent an autologous transplantation and 2 an allogeneic transplantation. Five-year PFS was estimated to 49% with 12 patients experiencing a relapse or progression including 7 patients with normal FDG-PET. Three patients with relapsed/progressive disease had an allogeneic transplant in second remission but subsequently died. Twelve patients died from disease-related causes and 3 from therapy-related causes, including 2 patients that developed secondary hematologic malignancies. Most relapses/progressions occurred in bone marrow, mediastinum or CNS with 3 patients with an isolated CNS relapse/progression. For the 7 patients receiving low intensity treatment (age 69–77 yrs) no patient survived beyond 30 months (median survival was 6.2 months), with 4 available for response evaluation, 2 achieving PR and 2 SD. For the whole cohort, age and female gender were identified as risk factors for shorter OS (HR 1.04, p=0.007 respectively HR 4.67, 0.001). Females were significantly older than males and for patients with intensive treatment, neither female gender nor age were any longer significant risk factors. This study is one of few to provide population-based data on treatment outcome of adult T-LBL. Age as a risk factor is likely to reflect intolerance to intensive treatment since age was not a risk factor for adverse OS or PFS for intensively treated patients. PET scan at time of response evaluation seems to be unreliable as predictor for the risk of relapse. Response rates in this material are comparable with published data while long term OS was slightly inferior, reflecting the population based nature of this data set. Disclosures: No relevant conflicts of interest to declare.


Author(s):  
Nabeel Khan ◽  
Tyler Pernes ◽  
Alexandra Weiss ◽  
Chinmay Trivedi ◽  
Manthankumar Patel ◽  
...  

Abstract Background The elderly inflammatory bowel disease (IBD) population has historically been under-represented in clinical trials, and data on the efficacy of biologic medications in elderly IBD patients are generally lacking. Our study aims to evaluate the efficacy of vedolizumab (VDZ) among elderly IBD patients and compare it with younger IBD patients in a nationwide population-based cohort of IBD patients. Methods We conducted a retrospective cohort study of patients within the US national Veterans Affairs Healthcare System (VAHS). Patients were stratified into 2 groups based on age at the time of starting VDZ (60 years of age and older or younger than 60 years of age) with outcomes compared between the 2 groups. The primary outcome was steroid-free remission during the 6- to 12-month period after starting VDZ therapy among those patients who were on steroids when VDZ was started. Results There were 568 patients treated with VDZ, of whom 56.7% had Crohn’s disease and 43.3% had ulcerative colitis. Among them, 316 patients were on steroids when VDZ was started. The percentage of patients who were on VDZ and off steroids during the 6- to 12-month period after VDZ initiation was 46.8% and 40.1% for the younger and elderly groups, respectively (P = 0.2374). Rates of hospitalization for an IBD-related reason within 1 year of VDZ start among the whole cohort were nearly identical in the younger and elderly groups (11.2% vs 11.3%, P = 0.9737). Rates of surgery for an IBD-related reason within 1 year of VDZ start were also similar between the young and elderly (3.9% vs 3.9%, P = 0.9851). Conclusions In a nationwide real-world retrospective cohort study of elderly IBD patients, we found that the efficacy of VDZ was similar among younger and older IBD patients and comparable with the published data in clinical trials.


Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2092
Author(s):  
Daria Hajka ◽  
Bartosz Budziak ◽  
Łukasz Pietras ◽  
Przemysław Duda ◽  
James A. McCubrey ◽  
...  

Glycogen synthase kinase 3 (GSK3) was initially isolated as a critical protein in energy metabolism. However, subsequent studies indicate that GSK-3 is a multi-tasking kinase that links numerous signaling pathways in a cell and plays a vital role in the regulation of many aspects of cellular physiology. As a regulator of actin and tubulin cytoskeleton, GSK3 influences processes of cell polarization, interaction with the extracellular matrix, and directional migration of cells and their organelles during the growth and development of an animal organism. In this review, the roles of GSK3–cytoskeleton interactions in brain development and pathology, migration of healthy and cancer cells, and in cellular trafficking of mitochondria will be discussed.


2020 ◽  
Vol 17 (5) ◽  
pp. 5120-5133
Author(s):  
Carl Graham ◽  
◽  
Jérôme Harmand ◽  
Sylvie Méléard ◽  
Josué Tchouanti ◽  
...  

2021 ◽  
Vol 107 (05) ◽  
pp. 227-233
Author(s):  
Bolli Þórsson ◽  
◽  
Elías Freyr Guðmundsson ◽  
Gunnar Sigurðsson ◽  
Thor Aspelund ◽  
...  

INTRODUCTION: The number of people with type 2 diabetes has increased in Iceland in the last few decades. We utilized the national database on prescribed medication from the Directorate of Health to estimate the prevalence and incidence of type 2 diabetes in Iceland and made prediction on the prevalence of type 2 diabetes in Iceland in 10 and 20 years. MATERIAL AND METHODS: Prevalence and incidence of type 2 diabetes for the period 2005-2018 was estimated based on prescriptions of diabetes medication in the national prescription database containing all prescriptions in Iceland during the period. The result was compared to the result from the REFINE-Reykjavik study (prospective, population-based cohort study) from 2004 to 2011 and published data from the USA from 1980 to 2016. RESULTS: The prevalence of type 2 diabetes more than doubled in near all age groups in both men and women in the period 2005-2018. The incidence increased by 2.8% annually (in 18-79 years old). The number of people in Iceland with type 2 diabetes was 10600 in 2018 and had increased from 4200 in the year 2005. Comparison with the results of the REFINE-Reykjavik study showed an underestimation (29% in men and women) of the prevalence of type 2 diabetes. If the increase in type 2 diabetes continues at a similar rate as in the years 2005-2018 the number of people with diabetes in Iceland could be near 24000 in the year 2040. CONCLUSION: Linear increase was seen in incidence and prevalence of people with type 2 diabetes in the years 2005-2018. Similar evolution was seen in USA from 1984. In order to counteract the increase of type 2 diabetes following the same path as has been seen in the USA, targeted measures are needed.


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