Prediction of High-Risk Types of Human Papillomaviruses Using Statistical Model of Protein “Sequence Space”

Abstract

Discrimination of high-risk types of human papillomaviruses plays an important role in the diagnosis and remedy of cervical cancer. Recently, several computational methods have been proposed based on protein sequence-based and structure-based information, but the information of their related proteins has not been used until now. In this paper, we proposed using protein “sequence space” to explore this information and used it to predict high-risk types of HPVs. The proposed method was tested on 68 samples with known HPV types and 4 samples without HPV types and further compared with the available approaches. The results show that the proposed method achieved the best performance among all the evaluated methods with accuracy 95.59% and F1-score 90.91%, which indicates that protein “sequence space” could potentially be used to improve prediction of high-risk types of HPVs.

The role of miR‐146a in viral infection

“…are responsible for cervical intraepithelial neoplasia and other oropharyngeal and anogenital cancers. HPV 16 and 18 are the two most common HPV strains known to be responsible for about 62.6 and 15.7% of cervical malignancy, respectively . HPV is a circular ds DNA virus, which encodes six early (E) proteins (E1, E2, E4, E5, E6, E7) and two late (L) proteins (L1, L2).…”

“…HPV is a circular ds DNA virus, which encodes six early (E) proteins (E1, E2, E4, E5, E6, E7) and two late (L) proteins (L1, L2). The two HPV oncoproteins, E6 and E7, are directly involved in the progression of HPV‐induced carcinogenesis …”

“…HPV 16 and 18 are the two most common HPV strains known to be responsible for about 62.6 and 15.7% of cervical malignancy, respectively. 107 HPV is a circular ds DNA virus, which encodes six early (E) proteins (E1, E2, E4, E5, E6, E7) and two late (L) proteins (L1, L2). The two HPV oncoproteins, E6 and E7, are directly involved in the progression of HPVinduced carcinogenesis.…”

“…The two HPV oncoproteins, E6 and E7, are directly involved in the progression of HPVinduced carcinogenesis. 105,107 Understanding the viability of the tumor cell and its basic mechanisms can be helpful to the development of effective therapeutic strategies. miRNAs, in this context, have been demonstrated to be associated with the cancer cells differentiation, viability, migration, adhesion, and apoptosis.…”

Polyploid Giant Cancer Cells, a Hallmark of Oncoviruses and a New Therapeutic Challenge

“…Besides, and based on their relative malignancy, HPVs are clustered into two types: low-risk (LR) HPV and high-risk (HR) HPV, where the former is linked to low-grade lesions as benign warts and the latter is interrelated to high-grade cervical lesions and cancers ( 16 ). Although HR HPV are further divided into 20 types ( 17 ), HPV-16 and−18 are the most studied ones as they account for 62.6 and 15.7% of cervical cancer cases respectively, with a special highlight on the two HPV-encoded oncoproteins E6 and E7 ( 18 , 19 ). In this context, the detection of polyploidy is finely described.…”