Publikasi Scopus 2024 per tanggal 31 Maret 2024 (233 artikel)

Handoko; Adham M.; Rachmadi L.; Wibowo H.; Gondhowiardjo S.A.
Handoko (57209984822); Adham, Marlinda (14024202100); Rachmadi, Lisnawati (55062422000); Wibowo, Heri (57217690943); Gondhowiardjo, Soehartati A. (6508327402)
57209984822; 14024202100; 55062422000; 57217690943; 6508327402
Cold Tumour Phenotype Explained Through Whole Genome Sequencing in Clinical Nasopharyngeal Cancer: A Preliminary Study
2024
ImmunoTargets and Therapy
13
173
182
9
0
Department of Radiation Oncology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Department of Otorhinolaryngology-Head and Neck Surgery Department, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; Department of Anatomical Pathology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; Integrated Laboratory, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
Handoko, Department of Radiation Oncology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia, Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Adham M., Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia, Department of Otorhinolaryngology-Head and Neck Surgery Department, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; Rachmadi L., Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia, Department of Anatomical Pathology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia; Wibowo H., Integrated Laboratory, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Gondhowiardjo S.A., Department of Radiation Oncology, Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
Introduction: Nasopharyngeal cancer (NPC) is a complex cancer due to its unique genomic features and association with the Epstein–Barr virus (EBV). Despite therapeutic advancements, NPC prognosis remains poor, necessitating a deeper understanding of its genomics. Here, we present a comprehensive whole genome sequencing (WGS) view of NPC genomics and its correlation with the phenotype. Methods: This study involved WGS of a clinical NPC biopsy specimen. Sequencing was carried out using a long read sequencer from Oxford Nanopore. Analysis of the variants involved correlation with the phenotype of NPC. Results: A loss of genes within chromosome 6 from copy number variation (CNV) was found. The lost genes included HLA-A, HLA-B, and HLA-C, which work in the antigen presentation process. This loss of the major histocompatibility complex (MHC) apparatus resulted in the tumour’s ability to evade immune recognition. The tumour exhibited an immunologically “cold” phenotype, with mild tumour-infiltrating lymphocytes, supporting the possible etiology of loss of antigen presentation capability. Furthermore, the driver mutation PIK3CA gene was identified along with various other gene variants affecting numerous signaling pathways. Discussion: Comprehensive WGS was able to detect various mutations and genomic losses, which could explain tumour progression and immune evasion ability. Furthermore, the study identified the loss of other genes related to cancer and immune pathways, emphasizing the complexity of NPC genomics. In conclusion, this study underscores the significance of MHC class I gene loss and its probable correlation with the cold tumour phenotype observed in NPC. © 2024 Handoko et al.
antigen processing and presentation; copy number variation; deletion; genomic; MHC class I; nasopharyngeal cancer
alpelisib; fluorouracil; glutamic acid; major histocompatibility antigen class 1; amino acid sequence; antigen presentation; Article; bioinformatics; cancer growth; CD8+ T lymphocyte; chromosome 15; chromosome 6; copy number variation; DNA extraction; Epstein Barr virus; gene expression; gene mutation; genetic analysis; genetic screening; human; human tissue; KEGG; major histocompatibility complex; missense mutation; multiple cycle treatment; nasopharynx cancer; phagocytosis; phenotype; polymerase chain reaction; quality control; signal transduction; tumor growth; whole exome sequencing; whole genome sequencing
Dove Medical Press Ltd
22531556
Article
Q1
1681
1753