Evidence map›Paper›PMID 35502615›Full record

ArticleEpigenetics2022

Epigenetic aberrations of gene expression in a rat model of hepatocellular carcinoma.

Cayla Boycott, Megan Beetch, Tony Yang, Katarzyna Lubecka, Yuexi Ma, Jiaxi Zhang, Lucinda Kurzava Kendall, Melissa Ullmer, Benjamin S Ramsey, Sandra Torregrosa-Allen and 9 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Epigenetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.9field-weighted citation impact, top 29% 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

7 citing papers in PubMed, 10 citations in OpenAlex.

  1. Article
  2. A Mouse in vivo Model Mimicking MASH-Related HCC Pathogenesis.Journal of hepatocellular carcinoma · 2026
    Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Article
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

19 authors at 6 institutions in 3 countries.

Cayla BoycottFood, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
Megan BeetchFood, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
Tony YangFood, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
Katarzyna LubeckaDepartment of Biomedical Chemistry, Faculty of Health Sciences, Medical University of Lodz, Lodz, Poland.
Yuexi MaFood, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
Jiaxi ZhangFood, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
Lucinda Kurzava KendallDepartment of Nutrition Science, College of Health and Human Sciences, Purdue University, Indiana, USA.
Melissa UllmerDepartment of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
Benjamin S RamseyPurdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA.
Sandra Torregrosa-AllenPurdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA.
Bennett D ElzeyPurdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA.
Abigail CoxDepartment of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, Indiana, USA.
Nadia Atallah LanmanPurdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA.ORCID 0000-0002-1819-7070
Alisa HuiDepartment of Chemistry, Faculty of Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
Nathaniel VillanuevaDepartment of Chemistry, Faculty of Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
Aline de ContiDivision of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA.
Tao HuanDepartment of Chemistry, Faculty of Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
Igor PogribnyDivision of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA.
Barbara StefanskaFood, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
University of British Columbia · CAPurdue University West Lafayette · USNational Center for Toxicological Research · USIndiana University School of MedicineMedical University of Lodz · PLSt. Vincent Hospital · US

Funding

Tumor Microenvironment and Metastasis ProgramP30CA082709 · NCI · INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS · PI David W Clapp · 1999 to 2026
$59.3M
Transgenic Mouse Core Facility Shared Resource (TMCF-SR)P30CA023168 · NCI · PURDUE UNIVERSITY WEST LAFAYETTE · PI ANDREW D MESECAR · 1985 to 2026
$43.4M
NCI NIH HHS P30 CA023168NCI NIH HHS P30 CA082709
6 · The paper itself

Abstract

Hepatocellular carcinoma (HCC) is mostly triggered by environmental and life-style factors and may involve epigenetic aberrations. However, a comprehensive documentation of the link between the dysregulated epigenome, transcriptome, and liver carcinogenesis is lacking. In the present study, Fischer-344 rats were fed a choline-deficient (CDAA, cancer group) or choline-sufficient (CSAA, healthy group) L-amino acid-defined diet. At the end of 52 weeks, transcriptomic alterations in livers of rats with HCC tumours and healthy livers were investigated by RNA sequencing. DNA methylation and gene expression were assessed by pyrosequencing and quantitative reverse-transcription PCR (qRT-PCR), respectively. We discovered 1,848 genes that were significantly differentially expressed in livers of rats with HCC tumours (CDAA) as compared with healthy livers (CSAA). Upregulated genes in the CDAA group were associated with cancer-related functions, whereas macronutrient metabolic processes were enriched by downregulated genes. Changes of highest magnitude were detected in numerous upregulated genes that govern key oncogenic signalling pathways, including Notch, Wnt, Hedgehog, and extracellular matrix degradation. We further detected perturbations in DNA methylating and demethylating enzymes, which was reflected in decreased global DNA methylation and increased global DNA hydroxymethylation. Four selected upregulated candidates,

Indexed as

Carcinoma, HepatocellularLiver NeoplasmsAmino AcidsAnimalsCholineDNADNA MethylationEpigenesis, GeneticGene ExpressionHumansMatrix Metalloproteinase 12Mixed Function OxygenasesProto-Oncogene ProteinsRatsRats, Inbred F344Amino AcidsCholineDNAMatrix Metalloproteinase 12Mixed Function OxygenasesProto-Oncogene ProteinsTET1 protein, humanDNA methylationliver canceroncogenesTranscriptomics

Identifiers

PMID35502615
PMCPMC9586690
OpenAlexW4225386842

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.