Sains Malaysiana 50(12)(2021): 3667-3681

http://doi.org/10.17576/jsm-2021-5012-17

Proteomic Profile Mapping and Differential Expression of Protein in Ovarian Cancer

(Pemetaan Profil Proteomik dan Ungkapan Pembezaan Protein dalam Kanser Ovari)

AMBREEN TAUSEEF¹, ASIMA KARIM¹, GULFAM AHMAD², QURRATULANN AFZA GARDNER³ & MUHAMMAD WAHEED AKHTAR³*

¹Department of Physiology and Cell Biology, University of Health Sciences, Lahore, Pakistan

²School of Medical Sciences, Faculty of Medicine and Health, Sydney University, Australia

³School of Biological Sciences, University of the Punjab, Lahore, Pakistan

Received: 30 January 2021/Accepted: 30 March 2021

ABSTRACT

This study aimed to characterize differentially expressed proteins in malignant ovarian tissue to find out potential novel biomarkers in ovarian cancer (OC). We enrolled 20 ovarian cancer patients (40-65 years) and an equal number of age-matched healthy women to get malignant and healthy ovarian tissue samples for protein extraction and quantification after tissue lysis. The protein profile was analyzed using two-dimensional gel electrophoresis followed by MALDI-TOF mass spectrometry. Based on the information thus obtained, the proteins were identified using the relevant software and protein databank to analyze the malignant and non-malignant ovarian tissue samples (n = 20/group). In this proteomic analysis of the ovarian tissue, 112 proteins were detected. Based on a minimum of ≥ 1.5-fold expression difference (p-value ≤ 0.05; FDR ≤ 0.05 and PMF ≥ 79), 17 proteins were found to be upregulated while 27 were downregulated in the malignant ovarian tissue. Six of these proteins have not been previously reported in ovarian cancer. Out of these, three are upregulated while the other three are downregulated. The upregulated proteins are centrosomal protein of 290 kDa (Cep290), uncharacterized protein C1orf109 (C1orf109) and GTPase-activating Rap/Ran-GAP domain-like protein 3 (GARNL3), and the three downregulated proteins identified are actin-related protein 3 (ARP3), cytosolic carboxypeptidase 3 (AGBL3) and NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10 (NDUFA10). This proteomic mapping not only provides data on protein profiling of ovarian cancer in Pakistani population for the first time but also reports six novel differentially expressed proteins, which have not been previously reported in ovarian cancer patients. They may serve as potential novel biomarkers after further validation for early diagnosis and prognosis of ovarian cancer. It also provides additional data to improve existing knowledge of already reported protein ovarian cancer biomarkers.

Keywords: Mass spectrometry; ovarian cancer; proteomics; two-dimensional gel electrophoresis

ABSTRAK

Kajian ini bertujuan untuk mencirikan protein yang diekspreskan secara berbeza dalam tisu ovari ganas untuk mengetahui potensi penanda biologi baru dalam barah ovari (OC). Kami mendaftarkan 20 pesakit barah ovari (40-65 tahun) dan sebilangan wanita sihat yang sesuai dengan usia untuk mendapatkan sampel tisu ovari yang ganas dan sihat untuk pengambilan dan pengukuran protein setelah lisis tisu. Profil protein dianalisis menggunakan elektroforesis gel berdimensi dua diikuti dengan jisim spektrometri MALDI-TOF. Berdasarkan maklumat yang diperoleh, protein dikenal pasti menggunakan perisian dan pangkalan data protein yang relevan untuk menganalisis sampel tisu ovari yang ganas dan tidak ganas (n = 20/kumpulan). Dalam analisis proteomik tisu ovari ini, 112 protein dikesan. Berdasarkan perbezaan ekspresi minimum ≥ 1.5 gandaan perbezaan ungkapan (nilai p ≤ 0.05; FDR ≤ 0.05 dan PMF ≥ 79), 17 protein didapati diatur secara berlebihan sementara 27 diatur dengan lebih rendah pada tisu ovari malignan. Enam daripada protein ini belum pernah dilaporkan terkena kanser ovari. Daripada jumlah tersebut, tiga diatur lebih tinggi, sementara tiga yang lain diatur. Protein yang diatur adalah protein sentrosom 290 kDa (Cep290), protein C1orf109 yang tidak dicirikan (C1orf109 dan protein seperti domain 3/Rap-Ran-GAP yang mengaktifkan GTPase (GARNL3) dan tiga protein yang tidak terkawal yang dikenal pasti adalah protein yang berkaitan dengan aktin 3 (ARP3), sitosolik karboksipeptidase 3 (AGBL3) dan NADH dehidrogenase [ubiquinone] 1 subkompleks subunit alpha 10 (NDUFA10). Pemetaan proteomik ini tidak hanya memberikan data mengenai profil protein kanser ovari pada populasi Pakistan untuk pertama kalinya, tetapi juga melaporkan enam protein yang dinyatakan secara berbeza, yang sebelumnya tidak pernah dilaporkan pada pesakit barah ovari. Mereka boleh menjadi penanda biologi baru yang berpotensi setelah pengesahan lebih lanjut untuk diagnosis awal dan prognosis kanser ovari. Ia juga memberikan data tambahan untuk meningkatkan pengetahuan sedia ada mengenai penanda biologi kanser ovari protein yang sudah dilaporkan.

Kata kunci: Elektroforesis gel berdimensi dua; jisim spektrometri; kanser ovari; proteomik

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*Corresponding author; email: mwa.sbs@pu.edu.pk