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Kori M, Aydin B, Gulfidan G, Beklen H, Kelesoglu N, Caliskan Iscan A, Turanli B, Erzik C, Karademir B, Arga KY. The Repertoire of Glycan Alterations and Glycoproteins in Human Cancers. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:139-168. [PMID: 33404348 DOI: 10.1089/omi.2020.0210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer as the leading cause of death worldwide has many issues that still need to be addressed. Since the alterations on the glycan compositions or/and structures (i.e., glycosylation, sialylation, and fucosylation) are common features of tumorigenesis, glycomics becomes an emerging field examining the structure and function of glycans. In the past, cancer studies heavily relied on genomics and transcriptomics with relatively little exploration of the glycan alterations and glycoprotein biomarkers among individuals and populations. Since glycosylation of proteins increases their structural complexity by several orders of magnitude, glycome studies resulted in highly dynamic biomarkers that can be evaluated for cancer diagnosis, prognosis, and therapy. Glycome not only integrates our genetic background with past and present environmental factors but also offers a promise of more efficient patient stratification compared with genetic variations. Therefore, studying glycans holds great potential for better diagnostic markers as well as developing more efficient treatment strategies in human cancers. While recent developments in glycomics and associated technologies now offer new possibilities to achieve a high-throughput profiling of glycan diversity, we aim to give an overview of the current status of glycan research and the potential applications of the glycans in the scope of the personalized medicine strategies for cancer.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Busra Aydin
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Gizem Gulfidan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Hande Beklen
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Nurdan Kelesoglu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Ayşegul Caliskan Iscan
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey.,Department of Pharmacy, Istinye University, Istanbul, Turkey
| | - Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
| | - Can Erzik
- Department of Medical Biology and School of Medicine, Marmara University, Istanbul, Turkey
| | - Betul Karademir
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey.,Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
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Gu KN, Bang SY, Lee HS, Park Y, Kang JY, Kim JS, Nam B, Yoo HS, Shin JM, Lee YK, Lee TH, Chun S, Cho SK, Choi CB, Sung YK, Kim TH, Jun JB, Yoo DH, Kim K, Bae SC. Deletion at 2q14.3 is associated with worse response to TNF-α blockers in patients with rheumatoid arthritis. Arthritis Res Ther 2019; 21:195. [PMID: 31462329 PMCID: PMC6714408 DOI: 10.1186/s13075-019-1983-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/16/2019] [Indexed: 01/20/2023] Open
Abstract
Background Structural variations such as copy number variations (CNVs) have a functional impact on various human traits. This study profiled genome-wide CNVs in Korean patients with rheumatoid arthritis (RA) to investigate the efficacy of treatment with TNF-α blockers. Methods A total of 357 Korean patients with RA were examined for the efficacy of TNF-α blocker treatment. Disease activity indexes were measured at baseline and 6 months after the treatment. The patients were classified as responders and non-responders based on the change in disease activity indexes according to the EULAR response criteria. CNVs in the same patients were profiled using fluorescence signal intensity data generated by a genome-wide SNP array. The association of CNVs with response to TNF-α blockers was analyzed by multivariate logistic regression accounting for genetic background and clinical factors including body mass index, gender, baseline disease activity, TNF-α blocker used, and methotrexate treatment. Results The study subjects varied in their responses to TNF-α blockers and had 286 common CNVs in autosomes. We identified that the 3.8-kb deletion at 2q14.3 in 5% of the subjects was associated with response to TNF-α blockers (1.37 × 10− 5 ≤ P ≤ 4.07 × 10− 4) at a false discovery rate threshold of 5%. The deletion in the identified CNV was significantly more frequent in the non-responders than in the responders, indicating worse response to TNF-α blockers in the deletion carriers. The 3.8-kb deletion at 2q14.3 is located in an intergenic region with the binding sites of two transcription factors, MAFF and MAFK. Conclusions This study obtained the CNV landscape of Korean patients with RA and identified the common regional deletion associated with poor response to treatment with TNF-α blockers. Electronic supplementary material The online version of this article (10.1186/s13075-019-1983-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ki-Nam Gu
- Department of Biology, Kyung Hee University, Seoul, 02447, South Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Youngho Park
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea.,Department of Business Statistics, Hannam University, Daejeon, 34430, South Korea
| | - Ju-Yeon Kang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Ji-Soong Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Bora Nam
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Hyun-Seung Yoo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Jung-Min Shin
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Yeon-Kyung Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Tae-Han Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Sehwan Chun
- Department of Biology, Kyung Hee University, Seoul, 02447, South Korea
| | - Soo-Kyung Cho
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Chan-Bum Choi
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Yoon-Kyoung Sung
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Jae-Bum Jun
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Dae Hyun Yoo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, 02447, South Korea.
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea.
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