A Brief Analysis of PIK3CA Expression in Head and Neck Squamous Cell Carcinoma
* Rahman MM1, Manzur MR2, Afrin N3, Parvin A4, Yasmin M5, Uddin MM6, Khan J71. Dr. Md. Mizanur Rahman MBBS, M.Phil, PhDAssociate Professor, Department of Biochemistry, RMC.2. Dr. Md. Ruhul Manzur MBBS, M.Phil,
Assistant Professor, Department of Biochemistry, RMC.3. Dr. Nahida Afrin, MBBS, M.Phil, Assistant Professor,
Department of Biochemistry, RMC.4. Dr. Ayesha Parvin, MBBS, M.Phil, Lecturer,
Department of Biochemistry, RMC.5. Dr. Monira Yasmin, MBBS, M.Phil, Lecturer,
Department of Biochemistry, RMC.6. Dr. Mezbah Uddin, MBBS, M.Phil, Lecturer,
Department of Biochemistry, RMC.7. Dr. Md. Jahangir Khan, MBBS, M.Phil,
Associate Professor, Department of Biochemistry, Sheikh Hasina Medical College, Habiganj.Corresponding author: Dr. Md. Mizanur Rahman MBBS, M.Phil, PhD Associated Professor, Department of Biochemistry, Rangamati Medical College.Email: mizan2011bio@gmail.com
Abstract:Background: Head and neck squamous cell carcinoma (HNSCC) is the 6th common carcinoma worldwide. The PIK3CA gene is often dysregulated in many cancers including HNSCC. Here, we aimed to observe PIK3CA expression in HNSCC using publicly free common datasets like TCGA and using bioinformatics tool GEPIA2.Material and methods: Bioinformatics tools are often used to predict overall and survival analysis. Here, we used the TCGA dataset to examine PIK3CA expression. We use GEPIA2 to investigate PIK3CA gene expression in HNSCC patients to view overall and disease-free survival.Results: We observed that the most mutated gene is TP53with 266 (number of cases gene mutated) out of 378 (number of simple somatic mutation) in contrast to PIK3CA gene 63(number of cases gene mutated) out of 378 (number of simple somatic mutation). Overexpression of PIK3CA is related to a lower risk of death with treatment and a lower risk of disease recurrence.Conclusion: To understand the role played by the PIK3CA gene to establish a biomarker in head and neck squamous cell carcinoma (HNSCC).Keywords: HNSCC, PIK3CA, GEPIA2, TCGA.
Introduction:Head and Neck squamous cell carcinoma (HNSCC) is a heterogeneous cancer, arising from squamous cells of the mucous membrane of various anatomical regions including aero digestive tract, oral cavity, paranasal regions, nasopharynx, oropharynx, hypopharynx, larynx[1].The organs involved in speech, voice, smell, taste, and hearing—all essential structures for survival—can have their structure and function destroyed by HNSCC[2]. According to GLOBOCAN 2020, there are approximately 19.3 million new cancer cases and 10.0 million cancer deaths worldwide[3]. Head and neck cancer ranks sixth among all cancer types in the World with an incidence rate of 5.47% and a mortality rate of 5.13%[4]. Males are 60% more likely than females to get tobacco-related cancer (NICRH and BSMMU cancer registry data). Additionally, this registry shows that more than 60% of cancer cases occur in people between the ages of 30 and 65 [5]. According to another study, 20% or more of all malignancies in Bangladesh are HNSCC [6].PIK3CA (Phosphatidylinositol 3-Kinase) is located at chromosome 3 (cytogenetic band 3q26.32), which is composed of 85 KDa regulatory subunit and 110 kDa catalytic subunit. PIK3CA often mutated in many cancers including HNSCC may be a loss of 3p and gain of 8q at their position [7, 8]. In most cases mutated PIK3CA acts as an oncogene and is associated with HPV-associated HNSCC [9], resulting in the alteration of the cell cycle E2F1 gene[10].In HNSCC, there is 63% of mutations occur as reported previously [11]including 79 missense and 1 inframe mutation, and involve cell proliferation pathways [12, 13].In addition to HNSCC, PIK3CA mutations are also involved in PI3K/AKT/mTOR signaling pathways and are linked to colorectal and breast cancers. [14].PI3K/AKT/mTOR signaling pathways are significant, even though tumor homeostasis may follow any of the ten hallmarks of cancer. Therefore, using TCGA and GEPIA2 datasets, we investigated PIK3CA expression (part of PI3K/AKT/mTOR signaling pathways) in HNSCC in this study.Methods and materials:First, we used the freely accessible public database GDC Data Portal at the TCGA [15] program to try and find the genes that were highly expressed in HNSCC.Second, from GDC data portal, we selected exploration section and selected total 524 HNSCC cases [Other and unspecified part of tongue (130), larynx (115), other and ill-defined sites in lip, oral cavity (71), floor of mouth (56), tonsil (46), other and unspecified parts of mouth (43), base of tongue (24), gum (11), oropharynx (10), hypopharynx (9), palate (5), lip (3) and other and unspecified major salivary gland (1)]. Since our aim in the literature review was to look at PIK3CA in HNSCC, we looked at PIK3CA expression using the TCGA dataset. Third, we used the bioinformatics tool GEPIA2[16] to investigate PIK3CA gene expression to explore overall survival and disease-free survival.Results:1. Genes overexpressed in HNSCCUsing the GDC data portal, we investigated the top 10 genes out of 713 genes that are often overexpressed or mutated in HNSCC (Table 1). Among the top 10 overexpressed/mutated we selected PIK3CA which stands top 8th position. There are 524 HNSCC cases overall in the GDC data portal, but only 507 of those cases have all of the accessible data. There were 713 gene alterations, 6630 mutations, and primarily squamous cell type neoplasms among the 507 patients. In the instance of PIK3CA, there were 86 cases in which the gene was altered, 507 cases were examined for simple somatic mutations, and 35 cases in the cohort had a unique simple somatic mutation. This indicates that overexpression in the form of 35 distinct simple somatic mutations in the instance of PIK3CA occurs among the 507 cohort of HNSCC samples.Table I: List of top 10 genes commonly mutated in HNSCC
Mucin 16, associated
2. PIK3CA overexpressed in HNSCCWe use GEPIA2 (Gene Expression Profiling Interactive Analysis) to explore PIK3A expression in their dataset. In the GEPIA2 dataset overexpression of PIK3CA was found in the tumor (number of tumor tissues= 519) and number of normal tissues is 44; Expression value log2(TPM+1). Log2(TPM 1) in GEPIA2 represents gene expression level calculation, it is a logarithmic transformation of Transcripts Per Million (TPM). [TPM is transcript per kilobasemillion means how much RNA present in any sample, divided by RSEM (RNA sequence by expectation-maximization)]. PIK3CA is overexpressed in HNSCC tumors (red box) relative to normal tissue (grey box), with the number of instances shown by a dot as shownin Figure 1. Here, Log2FC (how one sample is different from another) cutoff value was 1 and p-value cutoff 0.01.This comprehensive analysis highlights TPM's diagnostic and prognostic significance in cancer, making it a valuable biomarker for disease detection and patient outcome prediction.
Introduction:Head and Neck squamous cell carcinoma (HNSCC) is a heterogeneous cancer, arising from squamous cells of the mucous membrane of various anatomical regions including aero digestive tract, oral cavity, paranasal regions, nasopharynx, oropharynx, hypopharynx, larynx[1].The organs involved in speech, voice, smell, taste, and hearing—all essential structures for survival—can have their structure and function destroyed by HNSCC[2]. According to GLOBOCAN 2020, there are approximately 19.3 million new cancer cases and 10.0 million cancer deaths worldwide[3]. Head and neck cancer ranks sixth among all cancer types in the World with an incidence rate of 5.47% and a mortality rate of 5.13%[4]. Males are 60% more likely than females to get tobacco-related cancer (NICRH and BSMMU cancer registry data). Additionally, this registry shows that more than 60% of cancer cases occur in people between the ages of 30 and 65 [5]. According to another study, 20% or more of all malignancies in Bangladesh are HNSCC [6].PIK3CA (Phosphatidylinositol 3-Kinase) is located at chromosome 3 (cytogenetic band 3q26.32), which is composed of 85 KDa regulatory subunit and 110 kDa catalytic subunit. PIK3CA often mutated in many cancers including HNSCC may be a loss of 3p and gain of 8q at their position [7, 8]. In most cases mutated PIK3CA acts as an oncogene and is associated with HPV-associated HNSCC [9], resulting in the alteration of the cell cycle E2F1 gene[10].In HNSCC, there is 63% of mutations occur as reported previously [11]including 79 missense and 1 inframe mutation, and involve cell proliferation pathways [12, 13].In addition to HNSCC, PIK3CA mutations are also involved in PI3K/AKT/mTOR signaling pathways and are linked to colorectal and breast cancers. [14].PI3K/AKT/mTOR signaling pathways are significant, even though tumor homeostasis may follow any of the ten hallmarks of cancer. Therefore, using TCGA and GEPIA2 datasets, we investigated PIK3CA expression (part of PI3K/AKT/mTOR signaling pathways) in HNSCC in this study.Methods and materials:First, we used the freely accessible public database GDC Data Portal at the TCGA [15] program to try and find the genes that were highly expressed in HNSCC.Second, from GDC data portal, we selected exploration section and selected total 524 HNSCC cases [Other and unspecified part of tongue (130), larynx (115), other and ill-defined sites in lip, oral cavity (71), floor of mouth (56), tonsil (46), other and unspecified parts of mouth (43), base of tongue (24), gum (11), oropharynx (10), hypopharynx (9), palate (5), lip (3) and other and unspecified major salivary gland (1)]. Since our aim in the literature review was to look at PIK3CA in HNSCC, we looked at PIK3CA expression using the TCGA dataset. Third, we used the bioinformatics tool GEPIA2[16] to investigate PIK3CA gene expression to explore overall survival and disease-free survival.Results:1. Genes overexpressed in HNSCCUsing the GDC data portal, we investigated the top 10 genes out of 713 genes that are often overexpressed or mutated in HNSCC (Table 1). Among the top 10 overexpressed/mutated we selected PIK3CA which stands top 8th position. There are 524 HNSCC cases overall in the GDC data portal, but only 507 of those cases have all of the accessible data. There were 713 gene alterations, 6630 mutations, and primarily squamous cell type neoplasms among the 507 patients. In the instance of PIK3CA, there were 86 cases in which the gene was altered, 507 cases were examined for simple somatic mutations, and 35 cases in the cohort had a unique simple somatic mutation. This indicates that overexpression in the form of 35 distinct simple somatic mutations in the instance of PIK3CA occurs among the 507 cohort of HNSCC samples.Table I: List of top 10 genes commonly mutated in HNSCC
| Gene Symbol | Gene name | Affected cases in cohort Number of cases where gene mutated/cases tested for simple somatic mutation | Number of Mutation (unique simple somatic mutation in the gene in the cohort) |
| TP53 | Tumor protein p53 | 357/507 (70.41%) | 267 |
| FAT1 | FAT atypical cadherin 1 | 116/507 (22.88%) | 138 |
| MUC16 | cell surface | 106/507 (20.91%) | 156 |
| CDKN2A | Cyclin-dependent kinase inhibitor 2A | 102/507 (20.12%) | 55 |
| CSMD3 | CUB and Sushi multiple domains 3 | 101/507 (19.92%) | 148 |
| NOTCH1 | Notch receptor 1 | 94/507 (18.54%) | 98 |
| LRP1B | LDL receptor-related protein1B | 95/507 (18.74%) | 124 |
| PIK3CA | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha | 86/507 (16.96%) | 35 |
| KMT2D | Lysine methyltransferase 2D | 71/507 (14.00%) | 79 |
| NSD1 | Nuclear receptor binding SETdomain protein 1 | 56/507 (11.05%) | 72 |
2. PIK3CA overexpressed in HNSCCWe use GEPIA2 (Gene Expression Profiling Interactive Analysis) to explore PIK3A expression in their dataset. In the GEPIA2 dataset overexpression of PIK3CA was found in the tumor (number of tumor tissues= 519) and number of normal tissues is 44; Expression value log2(TPM+1). Log2(TPM 1) in GEPIA2 represents gene expression level calculation, it is a logarithmic transformation of Transcripts Per Million (TPM). [TPM is transcript per kilobasemillion means how much RNA present in any sample, divided by RSEM (RNA sequence by expectation-maximization)]. PIK3CA is overexpressed in HNSCC tumors (red box) relative to normal tissue (grey box), with the number of instances shown by a dot as shownin Figure 1. Here, Log2FC (how one sample is different from another) cutoff value was 1 and p-value cutoff 0.01.This comprehensive analysis highlights TPM's diagnostic and prognostic significance in cancer, making it a valuable biomarker for disease detection and patient outcome prediction.
https://journal.swmc.edu.bd/article/original-article/jswmc2024v14-02-106Figure 1: Overexpression of PIK3CA observed in HNSCC.PIK3CA over expressed in HNSCC tumor (red) in comparison to normal tissue (grey) and dot represents number of incidence.3. Analysis of Overall Survival and Disease-free survivalFrom GEPIA2, we categorized total 518 HNSCC patients in to two group; low PIK3CA expression (259) and high PIK3CA group (259), where median cutoff value was 50% each (as default). In the case of an overall survival hazard ratio (HR) of 0.94; nearer to a 95% confidence interval, the log-rank p-value was 0.65. That means lower risk of death with treatment (HR 0.94 indicates 6% lower risk of death), although no significant difference observed in survival (log rank p value was 0.65). On the other hand, disease free survival hazard ratio is 0.83; log rank p value was 0.26. That means Hazard ratio of 0.83 indicates lower risk of disease recurrence and Log rank p value of 0.26 suggests no significant difference.
https://journal.swmc.edu.bd/article/original-article/jswmc2024v14-02-106
Figure 2: Comparison of overall and diseasefree survival among high and low PIK3CA expressed groups.Between patients with high and low expression of PIK3CA mutations in HNSCC, overall survival was 94% and diseasefree survival was 83%.DiscussionHead and Neck squamous cell carcinoma (HNSCC) is a heterogeneous devastating disease [17]. The five years’ overall survival of HNSCC is less than 50% [18] which warrants more importance for early diagnosis and monitoring of treatment outcome for this deadly disease. Therefore, the main purpose of our study was to establish a diagnostic biomarker in HNSCC. Our goal in this study was to examine PIK3CA expression in the TCGA dataset and evaluate overall and disease-free survival in GEPIA2 dataset.PIK3CA overexpressed in the TGCA dataset cohort (Table 1).PIK3CA overexpression observed in tumor tissue versus normal tissue from GEPIA2 datasets (Figures 1). PIK3CA overexpression influenced the overall and disease-free survival of HNSCC patients in GEPIA2 datasets resultinglower risk of death with treatment and lower risk of disease recurrence,although no significant difference observed in OS and DFS(Figure 2). Using bioinformatics tool like GEPIA2, we will be able to suggest that overexpression of PIK3CA resulting decreased risk of disease recurrence and lowered chance of mortality hence may be use as a biomarker in patients with HNSCC. Further research warranted to establish our suggestion.FundingThis work was not supported by any specific grant from any funding agencies in the public, commercial, or not-for-profit sectors.Conflicts of Interest DisclosureThe authors do not have any conflicts of interest to declare in relation to this work.References:1. Mehanna H, Paleri V, West CM, Nutting C. Head and neck cancer—part 1: epidemiology, presentation, and prevention. BMJ. 2010 Sep20; 341.doi: 10.1136/bmj.2. 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