Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier
Background: The reclassification of Papillary Thyroid Carcinoma (PTC) is an area of research that warrants attention. The connection between thyroid cancer, inflammation, and immune responses necessitates considering the mechanisms of differential prognosis of thyroid tumors from an immunological pe...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-05-01
|
| Series: | Translational Oncology |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1936523324000159 |
| _version_ | 1827321750978822144 |
|---|---|
| author | Hanlin Sun Zhengyan Chang Hongqiang Li Yifeng Tang Yihao Liu Lixue Qiao Guicheng Feng Runzhi Huang Dongyan Han De-tao Yin |
| author_facet | Hanlin Sun Zhengyan Chang Hongqiang Li Yifeng Tang Yihao Liu Lixue Qiao Guicheng Feng Runzhi Huang Dongyan Han De-tao Yin |
| author_sort | Hanlin Sun |
| collection | DOAJ |
| description | Background: The reclassification of Papillary Thyroid Carcinoma (PTC) is an area of research that warrants attention. The connection between thyroid cancer, inflammation, and immune responses necessitates considering the mechanisms of differential prognosis of thyroid tumors from an immunological perspective. Given the high adaptability of macrophages to environmental stimuli, focusing on the differentiation characteristics of macrophages might offer a novel approach to address the issues related to PTC subtyping. Methods: Single-cell RNA sequencing data of medullary cells infiltrated by papillary thyroid carcinoma obtained from public databases was subjected to dimensionality reduction clustering analysis. The RunUMAP and FindAllMarkers functions were utilized to identify the gene expression matrix of different clusters. Cell differentiation trajectory analysis was conducted using the Monocle R package. A complex regulatory network for the classification of Immune status and Macrophage differentiation-associated Papillary Thyroid Cancer Classification (IMPTCC) was constructed through quantitative multi-omics analysis. Immunohistochemistry (IHC) staining was utilized for pathological histology validation. Results: Through the integration of single-cell RNA and bulk sequencing data combined with multi-omics analysis, we identified crucial transcription factors, immune cells/immune functions, and signaling pathways. Based on this, regulatory networks for three IMPTCC clusters were established. Conclusion: Based on the co-expression network analysis results, we identified three subtypes of IMPTCC: Immune-Suppressive Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (ISMPTCC), Immune-Neutral Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (INMPTCC), and Immune-Activated Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (IAMPTCC). Each subtype exhibits distinct metabolic, immune, and regulatory characteristics corresponding to different states of macrophage differentiation. |
| first_indexed | 2024-03-07T23:06:09Z |
| format | Article |
| id | doaj.art-74332b37424b4d06953d74f4b85ff961 |
| institution | Directory Open Access Journal |
| issn | 1936-5233 |
| language | English |
| last_indexed | 2024-04-25T01:12:32Z |
| publishDate | 2024-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Translational Oncology |
| spelling | doaj.art-74332b37424b4d06953d74f4b85ff9612024-03-10T05:12:02ZengElsevierTranslational Oncology1936-52332024-05-0143101889Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifierHanlin Sun0Zhengyan Chang1Hongqiang Li2Yifeng Tang3Yihao Liu4Lixue Qiao5Guicheng Feng6Runzhi Huang7Dongyan Han8De-tao Yin9Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR ChinaDepartment of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR ChinaDepartment of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR ChinaDepartment of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR ChinaDepartment of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR ChinaDepartment of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR ChinaDepartment of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR ChinaDepartment of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, PR China; Corresponding author at: Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, 168 Changhai Road, Shanghai 200433, PR China.Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, PR China; Corresponding author at: Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai 200072, PR China.Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China; Engineering Research Center of Multidisciplinary Diagnosis and Treatment of Thyroid Cancer of Henan Province, Zhengzhou 450052, Henan, PR China; Key Medicine Laboratory of Thyroid Cancer of Henan Province, Zhengzhou 450052, Henan, PR China; Corresponding author at: Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, PR China.Background: The reclassification of Papillary Thyroid Carcinoma (PTC) is an area of research that warrants attention. The connection between thyroid cancer, inflammation, and immune responses necessitates considering the mechanisms of differential prognosis of thyroid tumors from an immunological perspective. Given the high adaptability of macrophages to environmental stimuli, focusing on the differentiation characteristics of macrophages might offer a novel approach to address the issues related to PTC subtyping. Methods: Single-cell RNA sequencing data of medullary cells infiltrated by papillary thyroid carcinoma obtained from public databases was subjected to dimensionality reduction clustering analysis. The RunUMAP and FindAllMarkers functions were utilized to identify the gene expression matrix of different clusters. Cell differentiation trajectory analysis was conducted using the Monocle R package. A complex regulatory network for the classification of Immune status and Macrophage differentiation-associated Papillary Thyroid Cancer Classification (IMPTCC) was constructed through quantitative multi-omics analysis. Immunohistochemistry (IHC) staining was utilized for pathological histology validation. Results: Through the integration of single-cell RNA and bulk sequencing data combined with multi-omics analysis, we identified crucial transcription factors, immune cells/immune functions, and signaling pathways. Based on this, regulatory networks for three IMPTCC clusters were established. Conclusion: Based on the co-expression network analysis results, we identified three subtypes of IMPTCC: Immune-Suppressive Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (ISMPTCC), Immune-Neutral Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (INMPTCC), and Immune-Activated Macrophage differentiation-associated Papillary Thyroid Carcinoma Classification (IAMPTCC). Each subtype exhibits distinct metabolic, immune, and regulatory characteristics corresponding to different states of macrophage differentiation.http://www.sciencedirect.com/science/article/pii/S1936523324000159Multi-omicsSingle-cell RNA sequencingPapillary thyroid carcinomaTumor immune microenvironmentMacrophage differentiation |
| spellingShingle | Hanlin Sun Zhengyan Chang Hongqiang Li Yifeng Tang Yihao Liu Lixue Qiao Guicheng Feng Runzhi Huang Dongyan Han De-tao Yin Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier Translational Oncology Multi-omics Single-cell RNA sequencing Papillary thyroid carcinoma Tumor immune microenvironment Macrophage differentiation |
| title | Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier |
| title_full | Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier |
| title_fullStr | Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier |
| title_full_unstemmed | Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier |
| title_short | Multi-omics analysis-based macrophage differentiation-associated papillary thyroid cancer patient classifier |
| title_sort | multi omics analysis based macrophage differentiation associated papillary thyroid cancer patient classifier |
| topic | Multi-omics Single-cell RNA sequencing Papillary thyroid carcinoma Tumor immune microenvironment Macrophage differentiation |
| url | http://www.sciencedirect.com/science/article/pii/S1936523324000159 |
| work_keys_str_mv | AT hanlinsun multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT zhengyanchang multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT hongqiangli multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT yifengtang multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT yihaoliu multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT lixueqiao multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT guichengfeng multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT runzhihuang multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT dongyanhan multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier AT detaoyin multiomicsanalysisbasedmacrophagedifferentiationassociatedpapillarythyroidcancerpatientclassifier |