A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer
Abstract Homology is a mathematical tool to quantify "the contact degree", which can be expressed in terms of Betti numbers. The Betti numbers used in this study consisted of two numbers, b0 (a zero-dimensional Betti number) and b1 (a one-dimensional Betti number). We developed a chromatin...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-46213-w |
| _version_ | 1797630227749273600 |
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| author | Yuhki Yokoyama Kazuki Kanayama Kento Iida Masako Onishi Tadasuke Nagatomo Mayu Ito Sachiko Nagumo Kunimitsu Kawahara Eiichi Morii Kazuaki Nakane Hirofumi Yamamoto |
| author_facet | Yuhki Yokoyama Kazuki Kanayama Kento Iida Masako Onishi Tadasuke Nagatomo Mayu Ito Sachiko Nagumo Kunimitsu Kawahara Eiichi Morii Kazuaki Nakane Hirofumi Yamamoto |
| author_sort | Yuhki Yokoyama |
| collection | DOAJ |
| description | Abstract Homology is a mathematical tool to quantify "the contact degree", which can be expressed in terms of Betti numbers. The Betti numbers used in this study consisted of two numbers, b0 (a zero-dimensional Betti number) and b1 (a one-dimensional Betti number). We developed a chromatin homology profile (CHP) method to quantify the chromatin contact degree based on this mathematical tool. Using the CHP method we analyzed the number of holes (surrounded areas = b1 value) formed by the chromatin contact and calculated the maximum value of b1 (b1MAX), the value of b1 exceeding 5 for the first time or Homology Value (HV), and the chromatin density (b1MAX/ns2). We attempted to detect differences in chromatin patterns and differentiate histological types of lung cancer from respiratory cytology using these three features. The HV of cancer cells was significantly lower than that of non-cancerous cells. Furthermore, b1MAX and b1MAX/ns2 showed significant differences between small cell and non-small cell carcinomas and between adenocarcinomas and squamous cell carcinomas, respectively. We quantitatively analyzed the chromatin patterns using homology and showed that the CHP method may be a useful tool for differentiating histological types of lung cancer in respiratory cytology. |
| first_indexed | 2024-03-11T11:05:12Z |
| format | Article |
| id | doaj.art-445c8984003d4240aa4761542462fecc |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-11T11:05:12Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-445c8984003d4240aa4761542462fecc2023-11-12T12:16:05ZengNature PortfolioScientific Reports2045-23222023-11-0113111010.1038/s41598-023-46213-wA quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancerYuhki Yokoyama0Kazuki Kanayama1Kento Iida2Masako Onishi3Tadasuke Nagatomo4Mayu Ito5Sachiko Nagumo6Kunimitsu Kawahara7Eiichi Morii8Kazuaki Nakane9Hirofumi Yamamoto10Department of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka UniversityDepartment of Clinical Nutrition, Suzuka University of Medical ScienceDepartment of Pathology, Osaka Habikino Medical CenterDepartment of Pathology, Osaka Habikino Medical CenterDepartment of Diagnostic Pathology, Osaka University HospitalDepartment of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka UniversityDepartment of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka UniversityDepartment of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka UniversityDepartment of Diagnostic Pathology, Osaka University HospitalDepartment of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka UniversityDepartment of Molecular Pathology, Division of Health Sciences, Graduate School of Medicine, Osaka UniversityAbstract Homology is a mathematical tool to quantify "the contact degree", which can be expressed in terms of Betti numbers. The Betti numbers used in this study consisted of two numbers, b0 (a zero-dimensional Betti number) and b1 (a one-dimensional Betti number). We developed a chromatin homology profile (CHP) method to quantify the chromatin contact degree based on this mathematical tool. Using the CHP method we analyzed the number of holes (surrounded areas = b1 value) formed by the chromatin contact and calculated the maximum value of b1 (b1MAX), the value of b1 exceeding 5 for the first time or Homology Value (HV), and the chromatin density (b1MAX/ns2). We attempted to detect differences in chromatin patterns and differentiate histological types of lung cancer from respiratory cytology using these three features. The HV of cancer cells was significantly lower than that of non-cancerous cells. Furthermore, b1MAX and b1MAX/ns2 showed significant differences between small cell and non-small cell carcinomas and between adenocarcinomas and squamous cell carcinomas, respectively. We quantitatively analyzed the chromatin patterns using homology and showed that the CHP method may be a useful tool for differentiating histological types of lung cancer in respiratory cytology.https://doi.org/10.1038/s41598-023-46213-w |
| spellingShingle | Yuhki Yokoyama Kazuki Kanayama Kento Iida Masako Onishi Tadasuke Nagatomo Mayu Ito Sachiko Nagumo Kunimitsu Kawahara Eiichi Morii Kazuaki Nakane Hirofumi Yamamoto A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer Scientific Reports |
| title | A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer |
| title_full | A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer |
| title_fullStr | A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer |
| title_full_unstemmed | A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer |
| title_short | A quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer |
| title_sort | quantitative evaluation method utilizing the homology concept to assess the state of chromatin within the nucleus of lung cancer |
| url | https://doi.org/10.1038/s41598-023-46213-w |
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