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Peer-reviewedCC BY 4.0PLOS One

Integrative transcriptomics and reverse network pharmacology prioritize DPP4 and Achyranthes bidentata in Barrett’s esophagus

  • Jiaying Wu1
  • Zhen Zheng2
  • Jiaming Wu
  1. 1School of Nursing, Ningbo College of Health Sciences, Ningbo, Zhejiang Province, China
  2. 2Department of Chemoradiation Oncology, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang Province, China
Open at sourcePDFDOICite

Abstract

Barrett's esophagus (BE) is a precursor of esophageal adenocarcinoma, but candidate expression markers and preventive hypotheses require evaluation across patients, cohorts, and evidence levels. We analyzed two GPL96 discovery cohorts comprising 15 matched normal–BE pairs, used pair-aware differential modeling and resampling, and rebuilt four external BE-tissue assessments from official GEO files. The primary analysis yielded 1,085 differentially expressed genes; LASSO selected 13 features, linear SVM-RFE selected 6, and pair-bootstrap Random Forest retained 20. DPP4 and CCRL2 were shared by the three primary feature sets, but not after phenotype-preserving ComBat sensitivity analysis. External Affymetrix AUCs were 1.000, 0.855, and 0.976 for DPP4 and 1.000, 0.858, and 0.963 for CCRL2. In the Illumina GSE28302 cohort, fixed-direction DPP4 AUC was 0.444 and CCRL2 lacked a uniquely mapped probe. Seventy-nine DEGs intersected the verified 710-gene disease union; STRING/CTD analysis ranked Niuxi, Mahuang, and Mahuanggen first through third. Reference-controlled docking advanced kaempferol–PPARG as the primary structural hypothesis and taxifolin–NQO1 as a secondary extension. Twelve 100 ns trajectories retained pocket-region contacts, but query compounds showed greater pose rearrangement than the reference ligands. These findings prioritize candidates for experimental validation and do not establish a diagnostic test, direct binding, expression reversal, or therapeutic efficacy.

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Cite

BibTeXRIS
BibTeX
@article{wu2026integrative,
  title = {{Integrative transcriptomics and reverse network pharmacology prioritize DPP4 and Achyranthes bidentata in Barrett’s esophagus}},
  author = {Jiaying Wu and Zhen Zheng and Jiaming Wu},
  journal = {PLOS One},
  year = {2026},
  month = sep,
  doi = {10.1371/journal.pone.0359324},
  url = {https://doi.org/10.1371/journal.pone.0359324},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Integrative transcriptomics and reverse network pharmacology prioritize DPP4 and Achyranthes bidentata in Barrett’s esophagus
AU  - Jiaying Wu
AU  - Zhen Zheng
AU  - Jiaming Wu
PY  - 2026
DA  - 2026/09/25
JO  - PLOS One
DO  - 10.1371/journal.pone.0359324
UR  - https://doi.org/10.1371/journal.pone.0359324
AB  - Barrett's esophagus (BE) is a precursor of esophageal adenocarcinoma, but candidate expression markers and preventive hypotheses require evaluation across patients, cohorts, and evidence levels. We analyzed two GPL96 discovery cohorts comprising 15 matched normal–BE pairs, used pair-aware differential modeling and resampling, and rebuilt four external BE-tissue assessments from official GEO files. The primary analysis yielded 1,085 differentially expressed genes; LASSO selected 13 features, linear SVM-RFE selected 6, and pair-bootstrap Random Forest retained 20. DPP4 and CCRL2 were shared by the three primary feature sets, but not after phenotype-preserving ComBat sensitivity analysis. External Affymetrix AUCs were 1.000, 0.855, and 0.976 for DPP4 and 1.000, 0.858, and 0.963 for CCRL2. In the Illumina GSE28302 cohort, fixed-direction DPP4 AUC was 0.444 and CCRL2 lacked a uniquely mapped probe. Seventy-nine DEGs intersected the verified 710-gene disease union; STRING/CTD analysis ranked Niuxi, Mahuang, and Mahuanggen first through third. Reference-controlled docking advanced kaempferol–PPARG as the primary structural hypothesis and taxifolin–NQO1 as a secondary extension. Twelve 100 ns trajectories retained pocket-region contacts, but query compounds showed greater pose rearrangement than the reference ligands. These findings prioritize candidates for experimental validation and do not establish a diagnostic test, direct binding, expression reversal, or therapeutic efficacy.
SN  - 1932-6203
ER  -