DOI: 10.5061/dryad.q573n5tsr
title: Analysis of EGFR signaling pathway; miRNAs and inflammatory biomarkers in a high-risk oral cancer population in Pakistan

description: 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&lt;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&lt;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.
description: 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&lt;0.05 and 95%
 CI).<strong> </strong>
description: # Analysis of EGFR signaling pathway; miRNAs and inflammatory biomarkers
 in a high-risk oral cancer population in Pakistan
 [https://doi.org/10.5061/dryad.q573n5tsr](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&lt;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.