Evidence map›Paper›PMID 40632306›Full record

ArticleFunctional & integrative genomics2025

Integrated Nanopore and short-read RNA sequencing identifies dysregulation of METTL3- m6A modifications in endocrine therapy- sensitive and resistant breast cancer cells.

Belinda J Petri, Kellianne M Piell, Bailey L Avila-Valdes, Christian G Stanley, Laura J Winkler, Johnny Tyler Brown, Rye Ulett, Gabriela Sanchez, Julia H Chariker, Eric C Rouchka and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Functional & integrative genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
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

4 citing papers in PubMed.

  1. Regulation of PSAT1 and PHGDH by m6A in endocrine-resistant breast cancer cells.Biochimica et biophysica acta. Molecular basis of disease · 2026
    Article
  2. Review
  3. Article
  4. Review
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

11 authors.

Belinda J PetriDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Kellianne M PiellDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Bailey L Avila-ValdesDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Christian G StanleyDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Laura J WinklerDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Johnny Tyler BrownDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Rye UlettDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Gabriela SanchezDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Julia H CharikerKentucky IDeA Networks of Biomedical Research Excellence Bioinformatics Core, University of Louisville School of Medicine, Louisville, KY, USA.
Eric C RouchkaDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
Carolyn M KlingeDepartment of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA. carolyn.klinge@louisville.edu.

Funding

WKU Lead Faculty AwardP20GM103436 · NIGMS · UNIVERSITY OF LOUISVILLE · PI ERIC C ROUCHKA · 2012 to 2026
$60.1M
Summer Endocrine Research Training ProgramT35DK072923 · NIDDK · UNIVERSITY OF LOUISVILLE · PI KLINGE, CAROLYN M. · 2006 to 2025
$719k
National Institutes of Health National Institute of General Medical Sciences 5P20GM103436-22NIDDK NIH HHS T35 DK072923NIGMS NIH HHS P20 GM103436NIH HHS T35 DK072923Office of the Assistant Secretary of Defense for Health Affairs Breast Cancer Research Program HT9425-23-1-0017
6 · The paper itself

Abstract

The role of epitranscriptomic changes in the development of acquired endocrine therapy (ET)- resistance in estrogen receptor α (ER) expressing breast cancer (BC) is unknown. We tested the hypothesis that inhibition of METTL3, the methyltransferase responsible for the mRNA modification N-6 methyladenosine (m6A), alters m6A modifications and differentially regulates the abundance of mRNA transcripts in ET-sensitive MCF-7 versus resistant LCC9 ER + human BC cells. Differential m6A modifications were identified using direct mRNA sequencing (DRS) performed on five replicates for each cell line ± 1 µM STM2457, a selective METTL3 inhibitor, using Nanopore MinION long read RNA-seq. Parallel short read Illumina RNA-seq quantified differential transcript abundance in the same samples. Selected results were validated by RT-qPCR, m6A-RIP-qPCR, reporter assays, and western blot analysis. Statistical analysis combined m6Anet, a machine-learning algorithm designed to call m6A modified bases, with a generalized linear model following a binomial distribution analysis to identify significant differential m6A modification ratios (DMR). Distinct METTL3 dependent m6A modification patterns in LCC9 and MCF-7 cells were observed in differentially expressed genes (DEG) associated with ET-resistance, including EEF1A2, ACTB, FLNA, PDIA6, AMIGO2, TPT1, XBP1, and CITED4. Select results were validated in additional ET-resistant BC cell lines. m6A-RIP-RT-qPCR validated specific m6A sites. We examined the proximity of m6A sites to estrogen receptor α (ER α)-mRNA binding sites reported in MCF-7 cells. ACTB, PDIA6, and XBP1 demonstrated a short-range proximity, with m6A sites located within 100 bp of ERα binding sites, suggesting a role for m6A in influencing ERα-mRNA binding. Our work provides a framework for integrating DRS and DEG omics data. Our results suggest a role for dysregulation of m6A modifications in pathways implicated in ET resistance in BC.

Indexed as

AdenosineBreast NeoplasmsDrug Resistance, NeoplasmMethyltransferasesCell Line, TumorEstrogen Receptor alphaFemaleGene Expression Regulation, NeoplasticHumansMCF-7 CellsRNA, MessengerSequence Analysis, RNAAdenosineESR1 protein, humanEstrogen Receptor alphaMethyltransferasesMETTL3 protein, humanN-methyladenosineRNA, MessengerBreast cancerEndocrine-resistanceEpitranscriptomeM6ANanopore DRS

Identifiers

PMID40632306
PMCPMC12241209

What Socratic 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 Socratic graph.