Analysis of EGFR signaling pathway; miRNAs and inflammatory biomarkers in a high-risk oral cancer population in Pakistan
Data files
Jan 30, 2026 version files 5.92 KB
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Namra1(5.2.19)_for_analysis-working.sav
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README.md
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Abstract
Oral cancer has high morbidity rates in the Asian region, specifically Pakistan. However, little insight is available regarding the molecular pathogenesis and inflammatory biomarkers of this preventable cancer. This study determined the association of EGFR, NFκB, COX-2, and miRNAs expression with the chewing habits and high-risk human papillomavirus (HR-HPV) infection in oral cancer patients.**** Formalin-fixed embedded blocks (FFPPE) (n=50) were analyzed for transcriptional expression of EGFR, NFκB, and COX-2 by qPCR, and COX-2 protein expression was checked by immunohistochemistry (IHC). Array profiling of ~2500 miRNAs was performed on nine samples, and five miRNAs were selected for validation from this profiling data. Appropriate statistical tests were applied to check the association of EGFR., NFκB, COX-2, and miRNAs with chewing and HR-HPV status, (p<0.05 and 95% CI).**** Of the 50 samples, transcriptional expression of EGFR was observed in 13 (26%), NFκB in 11 (22%), and COX-2 in 17 (34%) samples, and the majority were chewers. EGFR and COX-2 expression were significantly associated with chewing gutka (the most carcinogenic form of chewing substance). A total of 281 miRNAs were dysregulated in miRNA profiling, and in validation, miR 222-3p was significantly downregulated in chewers expressing EGFR, NFκB, and COX-2 compared to non-chewers (p<0.05). HR-HPV positivity was not correlated with miRNAs. This study suggests a significant association of chewing habits with EGFR and COX-2 expression. In addition, the molecular pathogenesis of OSCC suggests the substantial interplay of NFκB, COX-2, EGFR and miRNAs in chronic chewers, irrespective of HR-HPV involvement.
https://doi.org/10.5061/dryad.q573n5tsr
Description of the data and file structure
Formalin-fixed embedded oral squamous cell carcinoma blocks (FFPPE) (n=50) were analyzed for transcriptional expression of EGFR, NFκB, and COX-2 by qPCR and COX-2 protein expression was checked by immunohistochemistry (IHC). Array profiling of ~2500 miRNAs was performed on nine samples, and five miRNAs were selected for validation from this profiling data. Appropriate statistical tests were applied to check the association of EGFR., NFκB, COX-2, and miRNAs with chewing and HR-HPV status, (p<0.05 and 95% CI).
Files and variables
File: Namra1(5.2.19)_for_analysis-working.sav
Description:
The file has variables of chewing habits, EGFR performed by FISH, HPV status, EGFR, COX-2, NFKB transcriptional expression, Gender, Smoking Record, and Tumor Stage.
Below is a description of each column of the SPSS file.
- Chewable_tobacco --- Are you having any addiction of chewable tobacco? Coded as Yes or No
- p16_IHC --- Immunohistochemistry expression of p16 protein. Coded as Negative and Positive
- EGFR_FISH ---Cytogenetics analysis of EGFR gene by FISH technique. Only 13 EGFR mRNA positive samples were processed for FISH analyses because of resource limitation. Dots in the EGFR_FISH columns represent Unchecked cases for EGFR FISH.
- EGFR --- Epidermal growth factor receptor mRNA expression was checked by qPCR and recorded as Negative and Positive
- HPV --- Human papillomavirus. The DNA presence was checked and recorded and Yes or No
- COX2_mRNA --- Transcriptional expression of COX-2 gene was checked by qPCR and recorded as Yes or No
- NfKB ---Transcriptional expression of NFkB was checked by qPCR and recorded as Yes or No
- COX2_IHC --- COX-2 Protein expression was checked by Immunohistochemistry analysis and coded as Positive and Negative
- Gender_rec ---- Gender of subjects
- Smoke_Rec --- If participants had/have smoking habits. Coded as Yes or No
- Tumor_site ---is grouped as Buccal mucosa and Non-buccal mucosa( all other parts of oral cavity)
- Stage --- grouped as Early stage (I,II) and Late stage (III, IV).
EGFR, NFKB, and COX-2 are genes and transcriptional expression was checked and recorded as Negative or Positive.
Code/software
SPSS was used for statistical analyses. JASP can be used to view the file.
Access information
Other publicly accessible locations of the data:
- Not applicable
Data was derived from the following sources:
- Not applicable
Human subjects data
All the data was collected after ethical approval from Aga Khan University Hospital ERC. Consent was obtained from the subjects, and the data is published keeping complete anonymity. No direct or indirect identifier is used which could breach the anonymity of the data.
Formalin-fixed embedded blocks (FFPPE) (n=50) were analyzed for transcriptional expression of EGFR, NFκB, and COX-2 by qPCR and COX-2 protein expression was checked by immunohistochemistry (IHC). Array profiling of ~2500 miRNAs was performed on nine samples, and five miRNAs were selected for validation from this profiling data. Appropriate statistical tests were applied to check the association of EGFR., NFκB, COX-2, and miRNAs with chewing and HR-HPV status, (p<0.05 and 95% CI).