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Guo D, Xie Q, Jiang S, Xie T, Li Y, Huang X, Li F, Wang T, Sun J, Wang A, Zhang Z, Li H, Bo X, Chen H, Liang Z. Synergistic alterations in the multilevel chromatin structure anchor dysregulated genes in small cell lung cancer. Comput Struct Biotechnol J 2021; 19:5946-5959. [PMID: 34849199 PMCID: PMC8604672 DOI: 10.1016/j.csbj.2021.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive form of lung cancer that uniquely changes the chromosomal structure, although the basis of aberrant gene expression in SCLC remains largely unclear. Topologically associated domains (TADs) are structural and functional units of the human genome. Genetic and epigenetic alterations in the cancer genome can lead to the disruption of TAD boundaries and may cause gene dysregulation. To understand the potential regulatory role of this process in SCLC, we developed the TAD boundary alteration-related gene identification in tumors (TARGET) computational framework, which enables the systematic identification of candidate dysregulated genes associated with altered TAD boundaries. Using TARGET to compare gene expression profiles between SCLC and normal human lung fibroblast cell lines, we identified >100 genes in this category, of which 24 were further verified in samples from patients with SCLC using NanoString. The analysis revealed synergistic chromatin structure alteration at the A/B compartment and TAD boundary levels that underlies aberrant gene expression in SCLC. TARGET is a novel and powerful tool that can be used to explore the relationship of chromatin structure alteration to gene dysregulation related to SCLC tumorigenesis, progression, and prognosis.
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Affiliation(s)
- Dan Guo
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Qiu Xie
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Shuai Jiang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Ting Xie
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yaru Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xin Huang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Fangyuan Li
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Tingting Wang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jian Sun
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Anqi Wang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zixin Zhang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hao Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hebing Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Sommer F. Rare Diseases of the Nose, the Paranasal Sinuses, and the Anterior Skull Base. Laryngorhinootologie 2021; 100:S1-S44. [PMID: 34352902 PMCID: PMC8354577 DOI: 10.1055/a-1331-2469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Due to their low incidence and thus resulting limited diagnostic criteria as well as therapeutic options, rare diseases of the nose, the paranasal sinuses, and the anterior skull base are a significant challenge. The value as of which a disease has to be considered as rare amounts to a maximum of 5 patients per 10 000 people. Within these diseases, however, there are extreme differences. Some rare or orphan diseases like for example the inverted papilloma belong to regularly diagnosed and treated diseases of larger departments of oto-rhino-laryngology whereas other rare diseases and malformations have only been described in less than 100 case reports worldwide. This fact emphasizes the necessity of bundling the available experience of diagnostics and therapy. The present article gives an overview about rare diseases of the nose, the paranasal sinuses, and the anterior skull base from the field of diseases/syndromes of the olfactory system, malformations of the nose and paranasal sinuses, ventilation and functional disorders as well as benign and malignant tumors. The classification and data on diagnostic and therapeutic options were established based on the current literature.
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Affiliation(s)
- Fabian Sommer
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Hals-Chirurgie, Universitätsklinik Ulm
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Abstract
Salivary gland diseases are rare. In the European Union (EU) a disease is considered to be rare if not more than 5 of 10,000 people are affected by it. According to estimates in Germany are about 4 million people with a rare disease. In the EU are about 30 million people with rare diseases [1]. In the present work most of the described diseases of salivary glands and of the facial nerve fall in this category. They form a very heterogeneous group whose treatment takes place mainly in specialized centers. Still, it is essential for the otolaryngologist to identify and to diagnose these diseases in order to initiate the right therapeutic steps. The work is a compilation of innate andacquired rare salivary gland disorders and of rare facial nerve disorders. The etiologies of inflammatory diseases, autoimmune disorders and tumors are taken into account. For the individual topics, the current literature, if available, was evaluated and turned into summarized facts. In this context the development of new processes, diagnostics, imaging and therapy are considered. Genetic backgrounds of salivary gland tumors and the trends in the treatment of tumorous lesions of the facial nerve are picked up. Furthermore, also rare diseases of the salivary glands in childhood are described. Some of them can occur in adults as well, but differ in frequency and symptoms. Due to the rarity of these diseases, it is recommended to tread these in centers with special expertise for it. Finally, the difficulties of initiation of studies and the problems of establishing disease registries concerning salivary gland disorders are discussed. This is very relevant because these pathologies are comparatively seldom.
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Affiliation(s)
- Claudia Scherl
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie,
Universitätsklinikum Mannheim
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