tailieunhanh - Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival

Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Research on HCC so far primarily focused on genes and provided limited information on genomic repeats, which constitute more than half of the human genome and contribute to genomic stability. In line with this, repeat dysregulation was significantly shown to be pathological in various cancers and other diseases. In this study, we aimed to determine the full repeat expression profile of HCC for the first time. We utilised two independent RNA-seq datasets obtained from primary HCC tumours with matched normal tissues of 20 and 17 HCC patients, respectively. We quantified repeat expressions and analysed their differential expression. We also identified repeats that are cooperatively expressed with genes by constructing a gene coexpression network. | Turkish Journal of Biology Turk J Biol 2021 45 599-612 http biology TÜBİTAK Research Article doi biy-2104-13 Identification of differentially expressed genomic repeats in primary hepatocellular carcinoma and their potential links to biological processes and survival 1 2 1 3 Gökhan KARAKÜLAH Cihangir YANDIM 1 İzmir Biomedicine and Genome Center İBG İzmir Turkey 2 İzmir International Biomedicine and Genome Institute İBG-İzmir Dokuz Eylül University İzmir Turkey 3 Department of Genetics and Bioengineering Faculty of Engineering İzmir University of Economics İzmir Turkey Received Accepted Published Online Final Version Abstract Hepatocellular carcinoma HCC is one of the deadliest cancers. Research on HCC so far primarily focused on genes and provided limited information on genomic repeats which constitute more than half of the human genome and contribute to genomic stability. In line with this repeat dysregulation was significantly shown to be pathological in various cancers and other diseases. In this study we aimed to determine the full repeat expression profile of HCC for the first time. We utilised two independent RNA-seq datasets obtained from primary HCC tumours with matched normal tissues of 20 and 17 HCC patients respectively. We quantified repeat expressions and analysed their differential expression. We also identified repeats that are cooperatively expressed with genes by constructing a gene coexpression network. Our results indicated that HCC tumours in both datasets harbour 24 differentially expressed repeats and even more elements were coexpressed with genes involved in various metabolic pathways. We discovered that two L1 elements L1M3b L1M3de were downregulated and a handful of HERV subfamily repeats HERV-Fc1-int HERV3-int HERVE_a-int HERVK11D-int HERVK14C-int HERVL18-int were upregulated with the exception of HERV1_LTRc which was downregulated. Various LTR elements LTR32 LTR9 LTR4 .

• Sinh học
• Journal of Biology
• Liver cancer
• Hepatocellular carcinoma
• Satellite RNA
• Transposable elements
• RNA sequencing
• Schizosaccharomyces pombe
• Mechanistic toxicology
• Cell biology
• Autophagy deficient cells
• Autophagosome formation
• Journal of Botany
• CRISPR/Cas9 system
• Model plants
• Plant biology
• Zinc finger nucleases
• Transcription activatorlike effector nucleases
• Large scale genetic screens
• Journal of Vietnam Agricultural Science and Technology
• Tạp chí Khoa học Công nghệ Nông nghiệp Việt Nam
• Piper nigrum
• Flower biology
• Anther dehiscence
• Stigma receptivity
• Turkish Journal of Biology
• Tạp chí Sinh học
• Doxorubicin induced transcriptome
• Systems biology
• DNA double strand breaks
• Reactive oxygen species
• báo cáo khoa học
• báo cáo hóa học
• công trình nghiên cứu về hóa học
• tài liệu về hóa học
• cách trình bày báo cáo
• trình bày báo cáo
• tài liệu báo cáo khoa học
• báo cáo y học
• kiến thức y học
• nghiên cứu y học
• Báo cáo sinh học hay
• báo cáo sinh học
• công trình nghiên cứu sinh học
• tài liệu về sinh học
• Quantitative Paleozoology
• Vertebrate Taphonomy
• Modern Ecological
• Conservation Biology
• biogeographic dynamics
• archaeological deposits
• Bài báo khoa học
• Academia Journal of Biology
• Động vật phù du
• Loài giáp xác râu
• Loài Grimaldina brazzai Richard
• Nuôi cấy sơ cấp
• Nuôi cấy tế bào
• Nguyên bào sợi
• Hiệu giá kháng thể
• Kháng thể đơn dòng kháng A
• Nhóm máu A
• Nhóm máu AB
• Tế bào lai
• Coptotermes gestroi
• DNA metagenome
• Endo 1 4 xylanase
• Glycoside hydrolase
• Nannochloropsis oculata
• Navicula tuscula
• Fatty acid
• Trachypithecus germaini
• Voọc bạc đông dương
• Núi đá vôi
• Thành phần loài
• Thảm thực vật
• New records of snakes
• Huu Lien nature reserve
• Reptile collection
• Cá ngựa vằn
• Phôi cá ngựa vằn
• Nhịp quẫy mình
• Danio rerio
• 16S rDNA
• Phylogenetic analyses
• Diversity of microcystins
• Non microcystin producing Microcystics population
• Protein chitinase
• Phương pháp bề mặt đáp ứng
• Sản xuất chitinase
• Tối ưu điều kiện biểu hiện
• Garcinia mangostana
• Độc tính tế bào
• Tế bào ung thư
• Cải biến gen
• Cây thuốc lá
• Gen cải biến gdhA
• Cây thuốc lá Nicotiana tabacum
• Gen độc lực
• Biểu hiện gen độc
• Chủng Salmonella
• Ngộ độc thực phẩm