In silico prediction of cancer immunogens: current state of the art

Doytchinova, Irini; Flower, Darren R.

doi:10.1186/s12865-018-0248-x

Cited by 9 publications

(3 citation statements)

References 58 publications

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“…Cancer is a chronic disease with varying degrees of manifestations characterized by abnormal cell division and high mortality and morbidity rates, in addition, it is considered the second leading cause of death worldwide with an estimated 8 million death annually and 18 million new cases per year [1][2][3][4][5]. Although the cancer survival rate increased dramatically over the years in many countries, yet more work are needed to improve the prognosis of patients suffering from this debilitating disease [6,7].…”

Section: Introductionmentioning

confidence: 99%

Immunoinformatics design of multiepitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

Abdelmoneim

Mustafa

Abdelmageed

et al. 2020

Immunological Medicine

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A new approach toward cancer therapy is the use of cancer vaccine, yet the different molecular bases of cancers, reduce the effectiveness of this approach. In this article, we aim to use matrix metalloproteinase-9 protein (MMP9) which is an essential molecule in the survival and metastasis of all types of cancers as a target for universal cancer vaccine design. The reference sequence of MMP9 protein was obtained from NCBI databases. Furthermore, the B-cell and T cell-related peptides were analyzed using the IEDB website and other related soft wares. The best candidate peptides were then visualized using chimera software. Three peptides were found to be good candidates for interactions with B cells (SLPE, RLYT, and PALPR), while 10 peptides were found as good targets for interactions with MHC1 and another 10 peptides founded suitable for interactions with MHC2 with population coverages of 94.77 and 90.67%, respectively. Finally, the immune response simulation and molecular docking were done using the C-IMMSIM simulator and AutoDock Vina to confirm the effectiveness of the proposed vaccine. By the end of this project: twenty-three peptide-based vaccine was designed for use as a universal cancer vaccine which has a high world population coverage for MHC1 (94.77%) and MHC2 (90.67%) related alleles.

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Section: Introductionmentioning

confidence: 99%

Immunoinformatics design of multiepitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

Abdelmoneim

Mustafa

Abdelmageed

et al. 2020

Immunological Medicine

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“…The core epitopes (YRYGYTRVA/ YGYTRVAEM) were noticed to be the dominant binders with 7 alleles for each(HLA-C*06:02,HLA-C*07:01,HLA-C*12:03,HLA-C*14:02,HLA-B*27:05,HLA-C*07:02,HLA-B*39:01/HLA-C*03:03,HLA-C*14:02,HLA-C*12:03,HLA-C*06:02,HLA-B*08:01,HLA-C*15:02,HLA-C*07:01). Followed by (YLYRYGYTR,WRFDVKAQM, ALWSAVTPL, LLLQKQLSL, LIADKWPAL, KLFGFCPTR, MYPMYRFTE, FLIADKWPA) which binds with (8, 5, 5, 3, 3, 5, 1, 3) alleles. (Table 3).…”

Section: Resultsmentioning

confidence: 99%

Immunoinformatic design of multi epitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

Abdelmoneim

Mustafa

Abdelmageed

et al. 2020

Preprint

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Background: Cancer remains a major public health hazard despite the extensive research over the years on cancer diagnostic and treatment , this is mainly due to the complex pathophysiology and genetic makeup of cancer. A new approach toward cancer treatment is the use of cancer vaccine, yet the different molecular bases of cancers reduce the effectiveness of this approach. In this work we aim to use matrix metalloproteinase-9 protein (MMP9) which is essential molecule in the survival and metastasis of all type of cancer as a target for universal cancer vaccine design. Method: reference sequence of matrix metalloproteinase-9 protein was obtained from NCBI databases along with the related sequence, which is then checked for conservation using BioEdit, furthermore the B cell and T cell related peptide were analyzed using IEDB website. The best candidate peptide were then visualized using chimera software. Result: Three Peptides found to be good candidate for interactions with B cells (SLPE, RLYT, and PALPR), while ten peptides found as a good target for interactions with MHC1 (YRYGYTRVA, YGYTRVAEM, YLYRYGYTR, WRFDVKAQM, ALWSAVTPL, LLLQKQLSL, LIADKWPAL, KLFGFCPTR , MYPMYRFTE, FLIADKWPA) with world combined coverage of 94.77% . In addition, ten peptides were also found as a good candidates for interactions with MHC2 (KMLLFSGRRLWRFDV, GRGKMLLFSGRRLWR, RGKMLLFSGRRLWRF, GKMLLFSGRRLWRFD, TFTRVYSRDADIVIQ, AVIDDAFARAFALWS, FARAFALWSAVTPLT, MLLFSGRRLWRFDVK, GNQLYLFKDGKYWRF, NQLYLFKDGKYWRFS), with world combined coverage of 90.67%. CONCLUSION: 23 peptide-based vaccine was designed for use as a universal cancer vaccine which has a high world population coverage for MHC1(94.77%) and MHC2 (90.67%) related alleles. Introduction:Cancer is a chronic disease with varying degree of manifestations characterized by abnormal cell division and high mortality and morbidity rates, in addition it is considered the second leading cause of death worldwide with an estimated 8 million death annually and 18 million new case per year.(1-5) although cancer survival rate increased dramatically over the years in many countries, yet more work are needed to improve the prognosis of patients suffering from this depilating disease.(6, 7) Cancer can be either common or rare depending on the number of cases. Usually any cancer with a number of cases below 6 in 100000 annually is considered rare type.(8) All types of cancers cause common clinical symptoms including weight-loss, fatigue, pain, nausea, vomiting and constipation, etc.(9)Additional symptoms are specific to the site of malignancy.(10) Breast cancer is the most common site of cancer in women worldwide.(11) Lung cancer is the second most common cancer in both men and women while colorectal is the third most common type cancer in both sexes. (12) The classical management for cancer composed of chemotherapy, radiotherapy and surgery. Recently Immunotherapy started to shows very promising result in field of cancer management. Different type of immunotherapy are available including cytokine therapy, ...

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“…In the present study, protein overexpression of HBXIP was demonstrated by searching a public database. In the latest research, public databases have been used for predicting cancer immunogens 32 and identifying candidate cancer biomarkers 33 . To the best of our knowledge, this is the first study to investigate HBXIP mRNA expression in human HNSCC using the Oncomine database, verify it with clinical samples, and then evaluate the clinicopathological characteristics and prognostic value of HBXIP.…”

Section: Discussionmentioning

confidence: 99%

Hepatitis B X‐interacting protein, involved in increasing proliferation and cell migration, is a prognostic marker in head and neck squamous cell carcinoma

Xue

Mori²,

Matsumoto

et al. 2021

Oral Science International

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Introduction Factors associated with prognosis and molecular mechanisms leading to a malignant phenotype in head and neck squamous cell carcinoma (HNSCC) need to be identified. The focus was on the biological function and clinical impact of hepatitis B X‐interacting protein (HBXIP) in HNSCC. Methods mRNA expression profiles of HBXIP were compared between tumor and normal tissues in head and neck cancer cases from an online database. The protein expressions of candidate genes were verified by immunohistochemistry (IHC) with tissue microarray blocks designed with 221 cases. Prognostic significance was analyzed using the Kaplan–Meier method and Cox regression analysis. The molecular function of malignant phenotypes was investigated by generating knockdown cell lines of HNSCC with RNA interference. Results Analysis of the online database showed that the mRNA of HBXIP was significantly higher in the HNSCC group than in normal specimens. IHC analysis showed significant differences in the protein expression of HBXIP by clinical stage, T status, and recurrence. Multivariate analysis showed that, in HBXIP IHC‐positive patients, N status, T status, and neural invasion were significantly associated with overall survival. In addition, downregulation of the HBXIP gene in SAS, a tongue squamous cancer cell line, inhibited proliferation and the invasion phenotype. Conclusions By increasing the malignant phenotypes of cell proliferation and invasion, upregulation of HBXIP was a prognostic factor in HNSCC.

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In silico prediction of cancer immunogens: current state of the art

Cited by 9 publications

References 58 publications

Immunoinformatics design of multiepitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

Immunoinformatics design of multiepitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

Immunoinformatic design of multi epitopes peptide-based universal cancer vaccine using matrix metalloproteinase-9 protein as a target

Hepatitis B X‐interacting protein, involved in increasing proliferation and cell migration, is a prognostic marker in head and neck squamous cell carcinoma

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