4.5 Article

'Social' versus 'asocial' cells-dynamic competition flux balance analysis

Related references

Note: Only part of the references are listed.
Article Endocrinology & Metabolism

Competitive, multi-objective, and compartmented Flux Balance Analysis for addressing tissue-specific inborn errors of metabolism

Yanhua Liu et al.

Summary: Inborn error of metabolism phenylketonuria (PKU) is typically caused by inactivation of phenylalanine hydroxylase (PAH). The reduced PAH activity results in elevated phenylalanine levels and phenylpyruvate in urine. Flux balance analysis (FBA) predicts reduced growth rate in PKU, unless tyrosine is supplemented. However, the PKU phenotype is brain-specific and can be treated by phenylalanine reduction instead of tyrosine supplementation. This study presents an extended FBA model that explains the brain specificity of the disease, the role of phenylpyruvate as a biomarker, the effect of excess phenylalanine on brain pathology, and the superiority of phenylalanine deprivation as therapy.

JOURNAL OF INHERITED METABOLIC DISEASE (2023)

Review Oncology

Hallmarks of Cancer: New Dimensions

Douglas Hanahan

Summary: The concept of the hallmarks of cancer is a tool for simplifying the complexity of cancer phenotypes and genotypes into basic principles. This article proposes phenotypic plasticity and disrupted differentiation as distinct hallmark capabilities, and discusses nonmutational epigenetic reprogramming and polymorphic microbiomes as enabling characteristics. Additionally, the importance of senescent cells in the tumor microenvironment is highlighted. The integrative concept of the hallmarks of cancer helps in understanding the mechanisms of cancer development and applying that knowledge to cancer medicine.

CANCER DISCOVERY (2022)

Review Gastroenterology & Hepatology

Liver regeneration: biological and pathological mechanisms and implications

George K. Michalopoulos et al.

Summary: The liver is a unique solid organ that uses regenerative mechanisms to maintain body homeostasis, unlike other solid organs that adjust to tissue loss but do not return to 100% of normal. This review discusses the regenerative pathways of the liver and the clinical implications of liver regeneration after injury.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2021)

Article Biochemistry & Molecular Biology

Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors

Joshua E. Lewis et al.

Summary: By analyzing redox metabolism at a systems level, it is possible to enhance radiation sensitivity and identify personalized metabolic targets for individual cancer patients.

CELL SYSTEMS (2021)

Article Multidisciplinary Sciences

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome

Akshit Goyal et al.

Summary: Combining ecology-based computational methods and optimization techniques, GutCP predicts a large number of experimentally untested cross-feeding interactions in the human gut microbiome. It has the potential to improve microbial community models and predict the metabolic profile of the gut.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines

Ewelina Weglarz-Tomczak et al.

Summary: Research has shown that the dependency of hepatocellular carcinoma on glucose/glutamine is associated with proliferation and lactate production, but does not necessarily increase with higher glucose concentration. Conversely, there is no such association with glutamine. The integration of gene expression and nutrient availability data into genome-wide models has been found to improve the prediction of metabolic phenotypes.

BIOMOLECULES (2021)

Review Biochemistry & Molecular Biology

Oral Selective Estrogen Receptor Degraders (SERDs) as a Novel Breast Cancer Therapy: Present and Future from a Clinical Perspective

Cristina Hernando et al.

Summary: ER+ breast cancer is the most common subtype, with endocrine therapy being the fundamental treatment. However, some patients develop endocrine resistance, with ESR1 gene mutations being a studied mechanism. SERDs have become a weapon against endocrine resistance in research and development, showing promise for improving patient outcomes.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Oncology

Hypoxia and the Tumor Microenvironment

Yue Li et al.

Summary: Hypoxia is a key feature of the tumor microenvironment, closely associated with cell proliferation, angiogenesis, metabolism, and the tumor immune response. These effects of hypoxia can further promote tumor progression, aggressiveness, metastatic potential, and lead to poor prognosis.

TECHNOLOGY IN CANCER RESEARCH & TREATMENT (2021)

Article Oncology

Exploring MYC relevance to cancer biology from the perspective of cell competition

Simona Paglia et al.

SEMINARS IN CANCER BIOLOGY (2020)

Article Biochemical Research Methods

Modeling microbial metabolic trade-offs in a chemostat

Zhiyuan Li et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

Article Biochemical Research Methods

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

Article Multidisciplinary Sciences

Enhanced oxidative phosphorylation in NKT cells is essential for their survival and function

Ajay Kumar et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Review Medicine, Research & Experimental

Analysis of the role of the Hippo pathway in cancer

Yanyan Han

JOURNAL OF TRANSLATIONAL MEDICINE (2019)

Article Mathematical & Computational Biology

Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network

Kazuhiro Maeda et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2019)

Review Gastroenterology & Hepatology

Hepatostat: Liver Regeneration and Normal Liver Tissue Maintenance

George K. Michalopoulos

HEPATOLOGY (2017)

Review Genetics & Heredity

MYC, Cell Competition, and Cell Death in Cancer: The Inseparable Triad

Simone Di Giacomo et al.

GENES (2017)

Article Multidisciplinary Sciences

Targeting pathogen metabolism without collateral damage to the host

Jurgen R. Haanstra et al.

SCIENTIFIC REPORTS (2017)

Article Multidisciplinary Sciences

Human Cancer Cells Signal Their Competitive Fitness Through MYC Activity

Simone Di Giacomo et al.

SCIENTIFIC REPORTS (2017)

Review Cell Biology

The Emerging Hallmarks of Cancer Metabolism

Natalya N. Pavlova et al.

CELL METABOLISM (2016)

Article Cell Biology

Dynamic flux balance analysis for synthetic microbial communities

Michael A. Henson et al.

IET SYSTEMS BIOLOGY (2014)

Article Multidisciplinary Sciences

Cell competition is a tumour suppressor mechanism in the thymus

Vera C. Martins et al.

NATURE (2014)

Article Multidisciplinary Sciences

MicroRNAs are critical regulators of tuberous sclerosis complex and mTORC1 activity in the size control of the Xenopus kidney

Daniel Romaker et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Mathematical & Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ali Ebrahim et al.

BMC SYSTEMS BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Dynamics of Hippocampal Neurogenesis in Adult Humans

Kirsty L. Spalding et al.

Review Oncology

Luminal breast cancer: from biology to treatment

Michail Ignatiadis et al.

NATURE REVIEWS CLINICAL ONCOLOGY (2013)

Article Cell Biology

Loss of Scribble causes cell competition in mammalian cells

Mark Norman et al.

JOURNAL OF CELL SCIENCE (2012)

Review Biochemistry & Molecular Biology

Hallmarks of Cancer: The Next Generation

Douglas Hanahan et al.

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

Involvement of Lgl and Mahjong/VprBP in Cell Competition

Yoichiro Tamori et al.

PLOS BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Engulfment is required for cell competition

Wei Li et al.

Review Oncology

The Myc oncoprotein as a therapeutic target for human cancer

Marina Vita et al.

SEMINARS IN CANCER BIOLOGY (2006)

Article Biochemistry & Molecular Biology

dMyc transforms cells into super-competitors

E Moreno et al.

Article Biophysics

Dynamic flux balance analysis of diauxic growth in Escherichia coli

R Mahadevan et al.

BIOPHYSICAL JOURNAL (2002)

Article Biotechnology & Applied Microbiology

Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments

AP Burgard et al.

BIOTECHNOLOGY PROGRESS (2001)