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Predictive analysis of BRAF V600E mutation and central lymph node metastasis in papillary thyroid carcinoma

  • Authors:
    • Junhui Peng
    • Zhihui Wu
    • Yujun Huang
    • Runhua Pan
    • Zhongdai Fu
    • Jianzhang Wang
  • View Affiliations / Copyright

    Affiliations: Department of General Surgery, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, Guangdong 528300, P.R. China, Department of Oncology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, Guangdong 528300, P.R. China, Department of Ultrasound, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, Guangdong 528300, P.R. China, Department of Pathology, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, Guangdong 528300, P.R. China
    Copyright: © Peng et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Article Number: 44
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    Published online on: November 24, 2025
       https://doi.org/10.3892/ol.2025.15397
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Abstract

The incidence of thyroid carcinoma (THCA) has risen, yet most nodules remain indolent. In classical papillary thyroid carcinoma (PTC), central lymph node metastasis (CLNM) strongly impacts recurrence and survival, highlighting the need for accurate preoperative risk assessment. The present study aimed to identify clinical and molecular predictors of CLNM, focusing on the BRAF V600E mutation, and to develop a personalized nomogram. Gene expression profiles and clinical data from TCGA were analyzed to identify BRAF V600E‑associated differentially expressed genes (DEGs) and construct a CLNM risk scoring model, which was further validated using retrospective preoperative fine‑needle aspiration cytology (FNAC) and postoperative immunohistochemistry specimens. BRAF V600E was highly prevalent, and associated DEGs showed moderate discriminatory power. Multivariate analysis identified age, tumor size, and high‑risk BRAF V600E status as independent predictors, integrated into a nomogram with an ROC of 0.710. Retrospective analyses confirmed the mutation's association with elevated CLNM risk. These findings suggest that patients with PTC with TI‑RADS ≥4a nodules and no radiologic cervical LNM may benefit from combined preoperative evaluation, including BRAF V600E testing via FNAC, enabling precise CLNM risk stratification and supporting individualized surgical planning.
View Figures

Figure 1

Figure 2

Landscape of BRAF mutations
and CLNM in PTC. (A) Pan-cancer distribution of BRAF
mutations across 32 tumor types in TCGA, with THCA showing the
highest frequency. (B) Waterfall plot of BRAF mutation types
in THCA, highlighting predominance of missense mutations. (C)
Lollipop plot showing amino acid mutation positions in THCA; V600E
is the most frequent variant. (D) CLNM incidence comparison between
BRAF V600E mutant and wild-type patients (P<0.001). (E)
Sankey diagram illustrating the relationship between BRAF
V600E mutation status and CLNM occurrence. CLNM, central lymph node
metastasis; PTC, papillary thyroid carcinoma; THCA, thyroid
carcinoma; TCGA, The Cancer Genome Atlas.

Figure 3

Differential gene expression and
functional enrichment in BRAF V600E PTC. (A) Volcano plot
showing significantly up- and downregulated genes between
BRAF V600E mutant and wild-type tumors. (B) Heatmap of top
DEGs stratified by mutation status. (C and D) KEGG and GO
enrichment analyses of upregulated genes highlighting thyroid
hormone biosynthesis and stress response pathways. (E and F) KEGG
and GO enrichment analyses of downregulated genes implicating
immune regulation and infection-related pathways. DEGs,
differentially expressed genes; KEGG, Kyoto Encyclopedia of Genes
and Genomes; GO, Gene Ontology.

Figure 4

Development and validation of a
diagnostic risk model for central lymph node metastasis based on
BRAF-associated DEGs. (A and B) LASSO regression and
cross-validation plots are used to identify the optimal gene
signature. (C and D) ROC and precision-recall curves showing model
performance in The Cancer Genome Atlas cohort (AUC=0.710). (E and
F) External validation using GSE60542 dataset (AUC=0.666). (G and
H) External validation using GSE29265 dataset (AUC=0.905),
confirming model generalizability. DEGs, differentially expressed
genes; LASSO, least absolute shrinkage and selection operator; ROC,
receiver operating characteristic; AUC, area under the curve.

Figure 5

Expression and predictive value of
model signature genes. (A) Boxplot comparing risk scores between
CLNM-positive (N1) and -negative (N0) patients, showing higher
scores in the metastatic group (P<0.001). (B) Heatmap of
signature gene expression across CLNM subgroups. (C) ROC curves
showing individual gene performance for CLNM prediction.
***P<0.001. CLNM, central lymph node metastasis; ROC, receiver
operating characteristic.

Figure 6

Association between risk score and
tumor immune microenvironment in THCA. (A) Correlation heatmap of
risk score with immune cell infiltration based on single-sample
Gene Set Enrichment Analysis. (B) Comparison of immune cell type
abundances between high- and low-risk groups. (C-E) Immune, stromal
and ESTIMATE scores, indicating higher immune/stromal content in
high-risk patients. (F and G) Differential expression of
interleukins, chemokines and receptors, mostly elevated in
high-risk patients. *P<0.05, **P<0.01, ***P<0.001. THCA,
thyroid carcinoma.

Figure 7

Immune checkpoint expression and IPS
comparison between risk groups. (A and B) Differential expression
of immune checkpoint inhibitors and stimulators in high- vs.
low-risk patients, with upregulation in the high-risk group. (C-F)
IPS analyses under four immunotherapy conditions
(PD-1+/CTLA4+, PD-1+/CTLA4−,
PD-1−/CTLA4+,
PD-1−/CTLA4−), indicating enhanced
immunogenicity in high-risk patients. IPS, immunophenoscore; PD-1,
programmed cell death protein 1; CTLA-4, cytotoxic T
lymphocyte-associated protein 4. *P<0.05, **P<0.01,
***P<0.001.

Figure 8

Construction and validation of a
nomogram for predicting CLNM in papillary thyroid carcinoma. (A)
Nomogram integrating age, T stage and risk score for individualized
prediction of CLNM probability. (B) Calibration plot demonstrating
agreement between predicted and observed probabilities
(C-index=0.769). (C) Restricted cubic spline analysis confirming
linear relationship between risk score and CLNM risk. (D) Decision
curve analysis showing net clinical benefit of combined model
compared with individual predictors. CLNM, central lymph node
metastasis; CI, confidence interval.

Figure 9

Predictive utility of preoperative
BRAF V600E testing via FNAC. (A) Flowchart of patient
inclusion and analysis for preoperative FNAC-based BRAF
V600E detection. (B) Comparison of CLNM incidence in patients with
and without BRAF V600E mutation, showing higher but
non-significant risk in mutant group. (C) Sankey diagram
illustrating CLNM distribution by BRAF mutation status.
FNAC, fine-needle aspiration cytology; CLNM, central lymph node
metastasis; PTC, papillary thyroid carcinoma.

Figure 10

Postoperative IHC detection of
BRAF V600E and CLNM association in PTC. (A) Flow diagram
summarizing postoperative cohort selection. (B) Representative IHC
images showed negative/weak/moderate/strong signal intensity of
BRAF V600E expression (scale bar, 100 µm). (C) Bar chart comparing
CLNM rates between BRAF-mutant and wild-type groups; higher
incidence observed in mutant group without statistical
significance. (D) Sankey diagram showing CLNM distribution
according to postoperative BRAF mutation status. CLNM,
central lymph node metastasis; PTC, papillary thyroid carcinoma;
IHC, immunohistochemistry.
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Copy and paste a formatted citation
Spandidos Publications style
Peng J, Wu Z, Huang Y, Pan R, Fu Z and Wang J: Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma. Oncol Lett 31: 44, 2026.
APA
Peng, J., Wu, Z., Huang, Y., Pan, R., Fu, Z., & Wang, J. (2026). Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma. Oncology Letters, 31, 44. https://doi.org/10.3892/ol.2025.15397
MLA
Peng, J., Wu, Z., Huang, Y., Pan, R., Fu, Z., Wang, J."Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma". Oncology Letters 31.1 (2026): 44.
Chicago
Peng, J., Wu, Z., Huang, Y., Pan, R., Fu, Z., Wang, J."Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma". Oncology Letters 31, no. 1 (2026): 44. https://doi.org/10.3892/ol.2025.15397
Copy and paste a formatted citation
x
Spandidos Publications style
Peng J, Wu Z, Huang Y, Pan R, Fu Z and Wang J: Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma. Oncol Lett 31: 44, 2026.
APA
Peng, J., Wu, Z., Huang, Y., Pan, R., Fu, Z., & Wang, J. (2026). Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma. Oncology Letters, 31, 44. https://doi.org/10.3892/ol.2025.15397
MLA
Peng, J., Wu, Z., Huang, Y., Pan, R., Fu, Z., Wang, J."Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma". Oncology Letters 31.1 (2026): 44.
Chicago
Peng, J., Wu, Z., Huang, Y., Pan, R., Fu, Z., Wang, J."Predictive analysis of <em>BRAF</em> V600E mutation and central lymph node metastasis in papillary thyroid carcinoma". Oncology Letters 31, no. 1 (2026): 44. https://doi.org/10.3892/ol.2025.15397
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