Evidence map›Paper›PMID 28202516›Full record

ArticleCancer research2017

Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation.

Linglin Yu, Mingyang Lu, Dongya Jia, Jianpeng Ma, Eshel Ben-Jacob, Herbert Levine, Benny Abraham Kaipparettu, José N Onuchic

Open access · greenAbstract read
In one paragraph

Article in Cancer research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 187 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
187citing papers in PubMed, 1 pooled it
8.9field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

187 citing papers in PubMed, 1 synthesis or guideline pooled it, 280 citations in OpenAlex.

  1. Pooled it
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  12. Vitamin B3 suppressesTranslational cancer research · 2026
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127 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 5 institutions in 2 countries.

Linglin YuCenter for Theoretical Biological Physics, Rice University, Houston, Texas.
Mingyang LuCenter for Theoretical Biological Physics, Rice University, Houston, Texas. jonuchic@rice.edu kaippare@bcm.edu mingyang.lu@jax.org.
Dongya JiaCenter for Theoretical Biological Physics, Rice University, Houston, Texas.
Jianpeng MaCenter for Theoretical Biological Physics, Rice University, Houston, Texas.
Eshel Ben-JacobCenter for Theoretical Biological Physics, Rice University, Houston, Texas.
Herbert LevineCenter for Theoretical Biological Physics, Rice University, Houston, Texas.
Benny Abraham KaipparettuDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas. jonuchic@rice.edu kaippare@bcm.edu mingyang.lu@jax.org.
José N OnuchicCenter for Theoretical Biological Physics, Rice University, Houston, Texas. jonuchic@rice.edu kaippare@bcm.edu mingyang.lu@jax.org.
Center for Theoretical Biological Physics · USBaylor College of Medicine · USChildren's Cancer Center · USJackson Laboratory · USTel Aviv University · IL

Funding

New Simulation Methods at Multi-Scales and -ResolutionsR01GM067801 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI MA, JIANPENG · 2003 to 2015
$3.4M
Molecular Mechanisms of Actin Cytoskeleton DynamicsR01GM116280 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI MA, JIANPENG, WANG, QINGHUA · 2016 to 2019
$1.4M
Mitochondria-nuclear crosstalk in triple negative breast cancer racial disparityR21CA179720 · NCI · BAYLOR COLLEGE OF MEDICINE · PI KAIPPARETTU, BENNY ABRAHAM · 2013 to 2015
$623k
Mitochondria specific metabolomic signature in triple negative breast cancer metaR21CA173150 · NCI · BAYLOR COLLEGE OF MEDICINE · PI KAIPPARETTU, BENNY ABRAHAM · 2013 to 2014
$369k
NCI NIH HHS R21 CA173150NCI NIH HHS R21 CA179720NIGMS NIH HHS R01 GM067801NIGMS NIH HHS R01 GM116280
6 · The paper itself

Abstract

Abnormal metabolism is a hallmark of cancer, yet its regulation remains poorly understood. Cancer cells were considered to utilize primarily glycolysis for ATP production, referred to as the Warburg effect. However, recent evidence suggests that oxidative phosphorylation (OXPHOS) plays a crucial role during cancer progression. Here we utilized a systems biology approach to decipher the regulatory principle of glycolysis and OXPHOS. Integrating information from literature, we constructed a regulatory network of genes and metabolites, from which we extracted a core circuit containing HIF-1, AMPK, and ROS. Our circuit analysis showed that while normal cells have an oxidative state and a glycolytic state, cancer cells can access a hybrid state with both metabolic modes coexisting. This was due to higher ROS production and/or oncogene activation, such as RAS, MYC, and c-SRC. Guided by the model, we developed two signatures consisting of AMPK and HIF-1 downstream genes, respectively, to quantify the activity of glycolysis and OXPHOS. By applying the AMPK and HIF-1 signatures to The Cancer Genome Atlas patient transcriptomics data of multiple cancer types and single-cell RNA-seq data of lung adenocarcinoma, we confirmed an anticorrelation between AMPK and HIF-1 activities and the association of metabolic states with oncogenes. We propose that the hybrid phenotype contributes to metabolic plasticity, allowing cancer cells to adapt to various microenvironments. Using model simulations, our theoretical framework of metabolism can serve as a platform to decode cancer metabolic plasticity and design cancer therapies targeting metabolism.

Indexed as

GlycolysisOxidative PhosphorylationAMP-Activated Protein KinasesHumansHypoxia-Inducible Factor 1Models, BiologicalNeoplasmsProto-Oncogene Proteins c-mycReactive Oxygen SpeciesTumor MicroenvironmentAMP-Activated Protein KinasesHypoxia-Inducible Factor 1Proto-Oncogene Proteins c-mycReactive Oxygen Species

Identifiers

PMID28202516
PMCPMC5380541
OpenAlexW2588583440

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.