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Peer-reviewedCC BY-NC-NDBMC cancer

An R-loop-related gene signature predicts prognosis and shapes the immune microenvironment in esophageal squamous cell carcinoma.

  • Cui Meng1,2
  • Hong Su3
  • Ruiqing Yan4
  • Ruifang Sun5
  • Qianqian Yu5
  • Yongsheng Meng5
  • Yanfeng Xi6
6 affiliations
  1. 1Shanxi Medical University, Taiyuan, Shanxi, 030001, People's Republic of China.
  2. 2Department of Pathology, Sinopharm Tongmei General Hospital, Datong, Shanxi, 037003, People's Republic of China.
  3. 3Cancer Hospital Affiliated to Shanxi Medical University, Department of Pathology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, Shanxi, 030013, People's Republic of China.
  4. 4Department of Pharmacy, Sinopharm Tongmei General Hospital, Datong, Shanxi, 037003, People's Republic of China.
  5. 5Department of Tumor Biobank, Cancer Hospital Affiliated to Shanxi Medical University, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, Shanxi, 030013, People's Republic of China.
  6. 6Cancer Hospital Affiliated to Shanxi Medical University, Department of Pathology, Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, Shanxi, 030013, People's Republic of China. [email protected].
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Abstract

Background

Esophageal squamous cell carcinoma (ESCC) features a poor prognosis and unclear pathogenesis, and the role of R-loops, key regulators of genome stability, has not been systematically characterized in this disease.Methods

Transcriptomic and single-cell RNA sequencing data of ESCC were integrated with published R-loop-related genes (RLRGs) to construct an RLRG scoring system. The associations between the RLRG score and prognosis, tumor immune microenvironment, and tumor stemness were analyzed via multiple bioinformatics algorithms. The expression of core genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR), Western Blot, immunohistochemistry, and immunofluorescence.Results

Seven key RLRGs related to the prognosis of the ESCC patients were identified, among which three core genes-BRIX1, CHEK1, and NUP155-were significantly upregulated in ESCC tissues compared with controls, as confirmed by both bioinformatic analysis and experimental validation. Notably, BRIX1, CHEK1, and NUP155 were co-enriched in DNA replication, pyrimidine metabolism, RNA degradation, and MYC target pathways, which are closely linked to R-loop biology and suggest potential crosstalk between these genes and R-loop regulatory networks. Meanwhile, the low RLRGs score group exhibited significantly worse overall survival but displayed a more active yet dysfunctional immune microenvironment. Single-cell analysis identified SquamousEpithelium cells as the key cell type with the highest RLRG scores across five independent algorithms. Malignant SquamousEpithelium cells with high RLRG scores showed enhanced stemness and activation of pathways including JAK-STAT, hypoxia, and DNA repair.Conclusion

This study provided the first systematic characterization of the R-loop landscape in ESCC, suggests that SquamousEpithelium cells may play a key role in R-loop-associated progression and are identified as potential prognostic biomarkers with possible therapeutic relevance that requires functional validation.

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Cite

BibTeXRIS
BibTeX
@article{meng2026rlooprelated,
  title = {{An R-loop-related gene signature predicts prognosis and shapes the immune microenvironment in esophageal squamous cell carcinoma.}},
  author = {Cui Meng and Hong Su and Ruiqing Yan and Ruifang Sun and Qianqian Yu and Yongsheng Meng and Yanfeng Xi},
  journal = {BMC cancer},
  year = {2026},
  month = oct,
  doi = {10.1186/s12885-026-16564-4},
  url = {https://europepmc.org/article/MED/42926202},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - An R-loop-related gene signature predicts prognosis and shapes the immune microenvironment in esophageal squamous cell carcinoma.
AU  - Cui Meng
AU  - Hong Su
AU  - Ruiqing Yan
AU  - Ruifang Sun
AU  - Qianqian Yu
AU  - Yongsheng Meng
AU  - Yanfeng Xi
PY  - 2026
DA  - 2026/10/09
JO  - BMC cancer
DO  - 10.1186/s12885-026-16564-4
UR  - https://europepmc.org/article/MED/42926202
AB  - Background  Esophageal squamous cell carcinoma (ESCC) features a poor prognosis and unclear pathogenesis, and the role of R-loops, key regulators of genome stability, has not been systematically characterized in this disease.Methods  Transcriptomic and single-cell RNA sequencing data of ESCC were integrated with published R-loop-related genes (RLRGs) to construct an RLRG scoring system. The associations between the RLRG score and prognosis, tumor immune microenvironment, and tumor stemness were analyzed via multiple bioinformatics algorithms. The expression of core genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR), Western Blot, immunohistochemistry, and immunofluorescence.Results  Seven key RLRGs related to the prognosis of the ESCC patients were identified, among which three core genes-BRIX1, CHEK1, and NUP155-were significantly upregulated in ESCC tissues compared with controls, as confirmed by both bioinformatic analysis and experimental validation. Notably, BRIX1, CHEK1, and NUP155 were co-enriched in DNA replication, pyrimidine metabolism, RNA degradation, and MYC target pathways, which are closely linked to R-loop biology and suggest potential crosstalk between these genes and R-loop regulatory networks. Meanwhile, the low RLRGs score group exhibited significantly worse overall survival but displayed a more active yet dysfunctional immune microenvironment. Single-cell analysis identified SquamousEpithelium cells as the key cell type with the highest RLRG scores across five independent algorithms. Malignant SquamousEpithelium cells with high RLRG scores showed enhanced stemness and activation of pathways including JAK-STAT, hypoxia, and DNA repair.Conclusion  This study provided the first systematic characterization of the R-loop landscape in ESCC, suggests that SquamousEpithelium cells may play a key role in R-loop-associated progression and are identified as potential prognostic biomarkers with possible therapeutic relevance that requires functional validation.
SN  - 1471-2407
ER  -