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Lee M, Yoo TK, Chae BJ, Lee A, Cha YJ, Lee J, Ahn SG, Kang J. Luminal androgen receptor subtype and tumor-infiltrating lymphocytes groups based on triple-negative breast cancer molecular subclassification. Sci Rep 2024; 14:11278. [PMID: 38760384 PMCID: PMC11101432 DOI: 10.1038/s41598-024-61640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/08/2024] [Indexed: 05/19/2024] Open
Abstract
In our previous study, we developed a triple-negative breast cancer (TNBC) subtype classification that correlated with the TNBC molecular subclassification. In this study, we aimed to evaluate the predictor variables of this subtype classification on the whole slide and to validate the model's performance by using an external test set. We explored the characteristics of this subtype classification and investigated genomic alterations, including genomic scar signature scores. First, TNBC was classified into the luminal androgen receptor (LAR) and non-luminal androgen receptor (non-LAR) subtypes based on the AR Allred score (≥ 6 and < 6, respectively). Then, the non-LAR subtype was further classified into the lymphocyte-predominant (LP), lymphocyte-intermediate (LI), and lymphocyte-depleted (LD) groups based on stromal tumor-infiltrating lymphocytes (TILs) (< 20%, > 20% but < 60%, and ≥ 60%, respectively). This classification showed fair agreement with the molecular classification in the test set. The LAR subtype was characterized by a high rate of PIK3CA mutation, CD274 (encodes PD-L1) and PDCD1LG2 (encodes PD-L2) deletion, and a low homologous recombination deficiency (HRD) score. The non-LAR LD TIL group was characterized by a high frequency of NOTCH2 and MYC amplification and a high HRD score.
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Affiliation(s)
- Miseon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tae-Kyung Yoo
- Division of Breast Surgery, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Byung Joo Chae
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon Jin Cha
- Department of Pathology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute of Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Lee
- Cancer Research Institute, The Catholic University of Korea, Seoul, Republic of Korea
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung Gwe Ahn
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Institute for Breast Cancer Precision Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Jun Kang
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Wang B, Yu H, Gao J, Yang L, Zhang Y, Yuan X, Zhang Y. Machine learning deciphers the significance of mitochondrial regulators on the diagnosis and subtype classification in non-alcoholic fatty liver disease. Heliyon 2024; 10:e29860. [PMID: 38707433 PMCID: PMC11066337 DOI: 10.1016/j.heliyon.2024.e29860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Background Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent liver disease worldwide and lack of research on the diagnostic utility of mitochondrial regulators in NAFLD. Mitochondrial dysfunction plays a pivotal role in the development and progression of NAFLD, especially oxidative stress and acidity β-oxidative overload. Thus, we aimed to identify and validate a panel of mitochondrial gene expression biomarkers for detection of NAFLD. Methods We selected the GSE89632 dataset and identified key mitochondrial regulators by intersecting DEGs, WGCNA modules, and MRGs. Classification of NAFLD subtypes based on these key mitochondrial regulatory factors was performed, and the pattern of immune system infiltration in different NAFLD subtypes were also investigated. RF, LASSO, and SVM-RFE were employed to identify possible diagnostic biomarkers from key mitochondrial regulatory factors and the predictive power was demonstrated through ROC curves. Finally, we validated these potential diagnostic biomarkers in human peripheral blood samples and a high-fat diet-induced NAFLD mouse model. Results We identified 25 key regulators of mitochondria and two NAFLD subtypes with different immune infiltration patterns. Four potential diagnostic biomarkers (BCL2L11, NAGS, HDHD3, and RMND1) were screened by three machine learning methods thereby establishing the diagnostic model, which showed favorable predictive power and achieved significant clinical benefit at certain threshold probabilities. Then, through internal and external validation, we identified and confirmed that BCL2L11 was significantly downregulated in NAFLD, while the other three were significantly upregulated. Conclusion The four MRGs, namely BCL2L11, NAGS, HDHD3, and RMND1, are novel potential biomarkers for diagnosing NAFLD. A diagnostic model constructed using the four MRGs may aid early diagnosis of NAFLD in clinics.
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Affiliation(s)
- Bingyu Wang
- Heilongjiang University of Chinese Medicine, Harbin, China
- Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin, China
| | | | - Jiawei Gao
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Liuxin Yang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yali Zhang
- Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin, China
- Zhang Yali Famous Traditional Chinese Medicine Expert Studio, Harbin, China
| | - Xingxing Yuan
- Heilongjiang University of Chinese Medicine, Harbin, China
- Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin, China
| | - Yang Zhang
- Department of Gastroenterology, First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
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Matsumoto K, Fujimori N, Ichihara K, Takeno A, Murakami M, Ohno A, Kakehashi S, Teramatsu K, Ueda K, Nakata K, Sugahara O, Yamamoto T, Matsumoto A, Nakayama KI, Oda Y, Nakamura M, Ogawa Y. Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction. J Gastroenterol 2024:10.1007/s00535-024-02103-0. [PMID: 38684511 DOI: 10.1007/s00535-024-02103-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Recently, two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) have been proposed: the "Classical" and "Basal-like" subtypes, with the former showing better clinical outcomes than the latter. However, the "molecular" classification has not been applied in real-world clinical practice. This study aimed to establish patient-derived organoids (PDOs) for PDAC and evaluate their application in subtype classification and clinical outcome prediction. METHODS We utilized tumor samples acquired through endoscopic ultrasound-guided fine-needle biopsy and established a PDO library for subsequent use in morphological assessments, RNA-seq analyses, and in vitro drug response assays. We also conducted a prospective clinical study to evaluate whether analysis using PDOs can predict treatment response and prognosis. RESULTS PDOs of PDAC were established at a high efficiency (> 70%) with at least 100,000 live cells. Morphologically, PDOs were classified as gland-like structures (GL type) and densely proliferating inside (DP type) less than 2 weeks after tissue sampling. RNA-seq analysis revealed that the "morphological" subtype (GL vs. DP) corresponded to the "molecular" subtype ("Classical" vs. "Basal-like"). The "morphological" classification predicted the clinical treatment response and prognosis; the median overall survival of patients with GL type was significantly longer than that with DP type (P < 0.005). The GL type showed a better response to gemcitabine than the DP type in vitro, whereas the drug response of the DP type was improved by the combination of ERK inhibitor and chloroquine. CONCLUSIONS PDAC PDOs help in subtype determination and clinical outcome prediction, thereby facilitating the bench-to-bedside precision medicine for PDAC.
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Affiliation(s)
- Kazuhide Matsumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Nao Fujimori
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Ayumu Takeno
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masatoshi Murakami
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akihisa Ohno
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shotaro Kakehashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Katsuhito Teramatsu
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keijiro Ueda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kohei Nakata
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Osamu Sugahara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeo Yamamoto
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masafumi Nakamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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Fang W, Peng P, Lin K, Xiao F, He W, He M, Wei Q. m6A methylation modification and immune infiltration analysis in osteonecrosis of the femoral head. J Orthop Surg Res 2024; 19:183. [PMID: 38491545 PMCID: PMC10943872 DOI: 10.1186/s13018-024-04590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/28/2024] [Indexed: 03/18/2024] Open
Abstract
Osteonecrosis of the femoral head (ONFH) is a elaborate hip disease characterized by collapse of femoral head and osteoarthritis. RNA N6-methyladenosine (m6A) plays a crucial role in a lot of biological processes within eukaryotic cells. However, the role of m6A in the regulation of ONFH remains unclear. In this study, we identified the m6A regulators in ONFH and performed subtype classification. We identified 7 significantly differentially expressed m6A regulators through the analysis of differences between ONFH and normal samples in the Gene Expression Omnibus (GEO) database. A random forest algorithm was employed to monitor these regulators to assess the risk of developing ONFH. We constructed a nomogram based on these 7 regulators. The decision curve analysis suggested that patients can benefit from the nomogram model. We classified the ONFH samples into two m6A models according to these 7 regulators through consensus clustering algorithm. After that, we evaluated those two m6A patterns using principal component analysis. We assessed the scores of those two m6A patterns and their relationship with immune infiltration. We observed a higher m6A score of type A than that of type B. Finally, we performed a cross-validation of crucial m6A regulatory factors in ONFH using external datasets and femoral head bone samples. In conclusion, we believed that the m6A pattern could provide a novel diagnostic strategy and offer new insights for molecularly targeted therapy of ONFH.
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Affiliation(s)
- Weihua Fang
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peng Peng
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kun Lin
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fangjun Xiao
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei He
- Guangdong Research Institute for Orthopedics and Traumatology of Chinese Medicine, Guangzhou, China
- Department of Orthopaedics, The Third Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mincong He
- Guangdong Research Institute for Orthopedics and Traumatology of Chinese Medicine, Guangzhou, China.
- Department of Orthopaedics, The Third Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Qiushi Wei
- Guangdong Research Institute for Orthopedics and Traumatology of Chinese Medicine, Guangzhou, China.
- Department of Orthopaedics, The Third Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.
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5
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An Y, Liu X, Chen H, Wan G. [Identification of breast cancer subtypes based on graph convolutional network]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2024; 41:121-128. [PMID: 38403612 PMCID: PMC10894726 DOI: 10.7507/1001-5515.202306071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Identification of molecular subtypes of malignant tumors plays a vital role in individualized diagnosis, personalized treatment, and prognosis prediction of cancer patients. The continuous improvement of comprehensive tumor genomics database and the ongoing breakthroughs in deep learning technology have driven further advancements in computer-aided tumor classification. Although the existing classification methods based on gene expression omnibus database take the complexity of cancer molecular classification into account, they ignore the internal correlation and synergism of genes. To solve this problem, we propose a multi-layer graph convolutional network model for breast cancer subtype classification combined with hierarchical attention network. This model constructs the graph embedding datasets of patients' genes, and develops a new end-to-end multi-classification model, which can effectively recognize molecular subtypes of breast cancer. A large number of test data prove the good performance of this new model in the classification of breast cancer subtypes. Compared to the original graph convolutional neural networks and two mainstream graph neural network classification algorithms, the new model has remarkable advantages. The accuracy, weight-F1-score, weight-recall, and weight-precision of our model in seven-category classification has reached 0.851 7, 0.823 5, 0.851 7 and 0.793 6 respectively. In the four-category classification, the results are 0.928 5, 0.894 9, 0.928 5 and 0.865 0 respectively. In addition, compared with the latest breast cancer subtype classification algorithms, the method proposed in this paper also achieved the highest classification accuracy. In summary, the model proposed in this paper may serve as an auxiliary diagnostic technology, providing a reliable option for precise classification of breast cancer subtypes in the future and laying the theoretical foundation for computer-aided tumor classification.
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Affiliation(s)
- Yishuai An
- School of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Xiaojun Liu
- School of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Hengling Chen
- School of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Guihong Wan
- Department of Dermatology, Massachusetts General Hospital, Harvard University, Boston 02138, USA
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Zhang P, Chen H, Zhang Y, Liu Y, Zhu G, Zhao W, Shang Q, He J, Zhou Z, Shen G, Yu X, Zhang Z, Chen G, Yu F, Liang D, Tang J, Liu Z, Cui J, Jiang X, Ren H. Dry and wet experiments reveal diagnostic clustering and immune landscapes of cuproptosis patterns in patients with ankylosing spondylitis. Int Immunopharmacol 2024; 127:111326. [PMID: 38091828 DOI: 10.1016/j.intimp.2023.111326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024]
Abstract
Cuproptosis is a new manner of mitochondrial cell death induced by copper. There is evidence that serum copper has a crucial impact on ankylosing spondylitis (AS) by copper-induced inflammatory response. However, the molecular mechanisms of cuproptosis modulators in AS remain unknown. We aimed to use a bioinformatics-based method to comprehensively investigate cuproptosis-related subtype identification and immune microenvironment infiltration of AS. Additionally, we further verified the results by in vitro experiments, in which peripheral blood and fibroblast cells from AS patients were used to evaluate the functions of significant cuproptosis modulators on AS. Finally, eight significant cuproptosis modulators were identified by analysis of differences between controls and AS cases from GSE73754 dataset. Eight prognostic cuproptosis modulators (LIPT1, DLD, PDHA1, PDHB, SLC31A1, ATP7A, MTF1, CDKN2A) were identified using a random forest model for prediction of AS risk. A nomogram model of the 8 prognostic cuproptosis modulators was then constructed; the model could be beneficial in clinical settings, as indicated by decision curve analysis. Consensus clustering analysis was used to divide AS patients into two cuproptosis subtypes (clusterA & B) according to significant cuproptosis modulators. The cuproptosis score of each sample was calculated by principal component analysis to quantify cuproptosis subtypes. The cuproptosis scores were higher in clusterB than in clusterA. Additionally, cases in clusterA were closely associated with the immunity of activated B cells, Activated CD4 T cell, Type17 T helper cell and Type2 T helper cell, while cases in clusterB were linked to Mast cell, Neutrophil, Plasmacytoid dendritic cell immunity, indicating that clusterB may be more correlated with AS. Notably, key cuproptosis genes including ATP7A, MTF1, SLC31A1 detected by RT-qPCR with peripheral blood exhibited significantly higher expression levels in AS cases than controls; LIPT1 showed the opposite results; High MTF1 expression is correlated with increased osteogenic capacity. In general, this study of cuproptosis patterns may provide promising biomarkers and immunotherapeutic strategies for future AS treatment.
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Affiliation(s)
- Peng Zhang
- The Second Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Honglin Chen
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - You Zhang
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yu Liu
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Guangye Zhu
- Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou 215007, China
| | - Wenhua Zhao
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Qi Shang
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jiahui He
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou 510130, China
| | - Zelin Zhou
- The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Gengyang Shen
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Xiang Yu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Zhida Zhang
- The Affiliated TCM Hospital of Guangzhou Medical University, Guangzhou 510130, China
| | - Guifeng Chen
- Shanghai 9th Peoples Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200011, China
| | - Fuyong Yu
- Qianxinan Autonomous Prefecture Hospital of TCM, Xingyi 562400, China
| | - De Liang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jingjing Tang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Zhixiang Liu
- Affiliated Huadu Hospital, Southern Medical University, Guangzhou 510800, China
| | - Jianchao Cui
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Xiaobing Jiang
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
| | - Hui Ren
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
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O'Malley KJ, Alnablsi MW, Xi Y, Pathak M, Khan F, Pillai AK, Kathuria MK, Vongpatanasin W. Diagnostic performance of the adrenal vein to inferior vena cava aldosterone ratio in classifying the subtype of primary aldosteronism. Hypertens Res 2023; 46:2535-2542. [PMID: 37673958 DOI: 10.1038/s41440-023-01421-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/30/2023] [Accepted: 08/20/2023] [Indexed: 09/08/2023]
Abstract
Adrenal vein sampling (AVS) is the standard procedure for distinguishing unilateral primary aldosteronism (PA) from bilateral PA. In cases where only one adrenal vein is successfully cannulated, it has been suggested that subtype classification can be determined based on the ratio of the concentration of aldosterone between the adrenal vein and the inferior vena cava (AV/IVC index). However, diagnostic performance of the ipsilateral versus contralateral AV/IVC index in predicting lateralization has not been directly compared. In a retrospective cohort of 133 patients with confirmed PA who underwent successful AVS, the performance of the AV/IVC index to predict laterality was evaluated and the area under the receiver operating characteristic (AUROC) curves was calculated. In detecting left unilateral PA (n = 47), the AUROC of the right AV/IVC index (RAV/IVC) was significantly higher than the AUROC of the left AV/IVC (LAV/IVC) index (0.967 vs. 0.871, p = 0.008). In detecting right unilateral PA (n = 30), the AUROC of the LAV/IVC index tended to be higher than that of the RAV/IVC index, but the difference did not reach statistical significance (0.966 vs. 0.906, p = 0.08). In detecting left unilateral PA, the sensitivities of the RAV/IVC and LAV/IVC indices were 83% and 46%, respectively, while the specificities of both were above 90%. In detecting right unilateral PA, the sensitivities of the LAV/IVC and RAV/IVC indices were 80% and 43%, respectively, while the specificities of both were above 90%. The AV/IVC index has superior diagnostic performance in detecting contralateral unilateral PA compared to ipsilateral unilateral PA.
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Affiliation(s)
- Kyle J O'Malley
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mhd W Alnablsi
- Department of Radiology (Division of Vascular Interventional Radiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yin Xi
- Department of Radiology (Division of Vascular Interventional Radiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mona Pathak
- Department of Pharmacotherapy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Fatima Khan
- Department of Radiology (Division of Vascular Interventional Radiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anil K Pillai
- Department of Radiology (Division of Vascular Interventional Radiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Manoj K Kathuria
- Department of Radiology (Division of Vascular Interventional Radiology), University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wanpen Vongpatanasin
- Department of Internal Medicine (Division of Cardiology, Hypertension Section), University of Texas Southwestern, Dallas, TX, USA.
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Zhang H, Yang Y, Liu Z, Xu H, Zhu H, Wang P, Liang G. Significance of methylation-related genes in diagnosis and subtype classification of renal interstitial fibrosis. Hereditas 2023; 160:32. [PMID: 37496082 PMCID: PMC10373342 DOI: 10.1186/s41065-023-00295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND RNA methylation modifications, such as N1-methyladenosine/N6-methyladenosine /N5-methylcytosine (m1A/m6A/m5C), are the most common RNA modifications and are crucial for a number of biological processes. Nonetheless, the role of RNA methylation modifications of m1A/m6A/m5C in the pathogenesis of renal interstitial fibrosis (RIF) remains incompletely understood. METHODS Firstly, we downloaded 2 expression datasets from the GEO database, namely GSE22459 and GSE76882. In a differential analysis of these datasets between patients with and without RIF, we selected 33 methylation-related genes (MRGs). We then applied a PPI network, LASSO analysis, SVM-RFE algorithm, and RF algorithm to identify key MRGs. RESULTS We eventually obtained five candidate MRGs (WTAP, ALKBH5, YTHDF2, RBMX, and ELAVL1) to forecast the risk of RIF. We created a nomogram model derived from five key MRGs, which revealed that the nomogram model may be advantageous to patients. Based on the selected five significant MRGs, patients with RIF were classified into two MRG patterns using consensus clustering, and the correlation between the five MRGs, the two MRG patterns, and the genetic pattern with immune cell infiltration was shown. Moreover, we conducted GO and KEGG analyses on 768 DEGs between MRG clusters A and B to look into their different involvement in RIF. To measure the MRG patterns, a PCA algorithm was developed to determine MRG scores for each sample. The MRG scores of the patients in cluster B were higher than those in cluster A. CONCLUSIONS Ultimately, we concluded that cluster A in the two MRG patterns identified on these five key m1A/m6A/m5C regulators may be associated with RIF.
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Affiliation(s)
- Hanchao Zhang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Yue Yang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhengdao Liu
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Hong Xu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Han Zhu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Peirui Wang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Guobiao Liang
- Medical College of Soochow University, Suzhou, Jiangsu, China.
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China.
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Hu S, Shen C, Yao X, Zou Y, Wang T, Sun X, Nie M. m6A regulator-mediated methylation modification patterns and immune microenvironment infiltration characterization in osteoarthritis. BMC Med Genomics 2022; 15:273. [PMID: 36585683 PMCID: PMC9805027 DOI: 10.1186/s12920-022-01429-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023] Open
Abstract
Osteoarthritis (OA) is a common disease in orthopedics. RNA N6-methyladenosine (m6A) exerts an essential effect in a variety of biological processes in the eukaryotes. In this study, we determined the effect of m6A regulators in the OA along with performing the subtype classification. Differential analysis of OA and normal samples in the database of Gene Expression Omnibus identified 9 significantly differentially expressed m6A regulators. These regulators were monitored by a random forest algorithm so as to evaluate the risk of developing OA disease. On the basis of these 9 moderators, a nomogram was established. The results of decision curve analysis suggested that the patients could benefit from a nomogram model. The OA sample was classified as 2 m6A models through a consensus clustering algorithm in accordance with these 9 regulators. These 2 m6A patterns were then assessed with principal component analysis. We also determined the m6A scores for the 2 m6A patterns and their correlation with immune infiltration. The results indicated that type A had a higher m6A score than type B. Thus, we suggest that the m6A pattern may provide a new approach for diagnose and provide novel ideas for molecular targeted therapy of OA.
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Affiliation(s)
- Shidong Hu
- grid.412461.40000 0004 9334 6536Center for Joint Surgery, Department of Orthopedic Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, Yuzhong District, Chongqing, 400016 China
| | - Chen Shen
- grid.412461.40000 0004 9334 6536Center for Joint Surgery, Department of Orthopedic Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, Yuzhong District, Chongqing, 400016 China
| | - Xudong Yao
- grid.412461.40000 0004 9334 6536Center for Joint Surgery, Department of Orthopedic Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, Yuzhong District, Chongqing, 400016 China
| | - Yulong Zou
- grid.412461.40000 0004 9334 6536Center for Joint Surgery, Department of Orthopedic Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, Yuzhong District, Chongqing, 400016 China
| | - Ting Wang
- grid.412461.40000 0004 9334 6536Center for Joint Surgery, Department of Orthopedic Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, Yuzhong District, Chongqing, 400016 China
| | - Xianding Sun
- grid.412461.40000 0004 9334 6536Center for Joint Surgery, Department of Orthopedic Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, Yuzhong District, Chongqing, 400016 China
| | - Mao Nie
- grid.412461.40000 0004 9334 6536Center for Joint Surgery, Department of Orthopedic Surgery, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, Yuzhong District, Chongqing, 400016 China
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Guo Y, Song Q, Jiang M, Guo Y, Xu P, Zhang Y, Fu CC, Fang Q, Zeng M, Yao X. Histological Subtypes Classification of Lung Cancers on CT Images Using 3D Deep Learning and Radiomics. Acad Radiol 2021; 28:e258-e266. [PMID: 32622740 DOI: 10.1016/j.acra.2020.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/24/2022]
Abstract
RATIONALE AND OBJECTIVES Histological subtypes of lung cancers are critical for clinical treatment decision. In this study, we attempt to use 3D deep learning and radiomics methods to automatically distinguish lung adenocarcinomas (ADC), squamous cell carcinomas (SCC), and small cell lung cancers (SCLC) respectively on Computed Tomography images, and then compare their performance. MATERIALS AND METHODS 920 patients (mean age 61.2, range, 17-87; 340 Female and 580 Male) with lung cancer, including 554 patients with ADC, 175 patients with lung SCC and 191 patients with SCLC, were included in this retrospective study from January 2013 to August 2018. Histopathologic analysis was available for every patient. The classification models based on 3D deep learning (named the ProNet) and radiomics (named com_radNet) were designed to classify lung cancers into the three types mentioned above according to histopathologic results. The training, validation and testing cohorts counted 0.70, 0.15, and 0.15 of the whole datasets respectively. RESULTS The ProNet model used to classify the three types of lung cancers achieved the F1-scores of 90.0%, 72.4%, 83.7% in ADC, SCC, and SCLC respectively, and the weighted average F1-score of 73.2%. For com_radNet, the F1-scores achieved 83.1%, 75.4%, 85.1% in ADC, SCC, and SCLC, and the weighted average F1-score was 72.2%. The area under the receiver operating characteristic curve of the ProNet model and com_radNet were 0.840 and 0.789, and the accuracy were 71.6% and 74.7% respectively. CONCLUSION The ProNet and com_radNet models we developed can achieve high performance in distinguishing ADC, SCC, and SCLC and may be promising approaches for non-invasive predicting histological subtypes of lung cancers.
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Barnes BM, Nelson L, Tighe A, Burghel GJ, Lin IH, Desai S, McGrail JC, Morgan RD, Taylor SS. Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes. Genome Med 2021; 13:140. [PMID: 34470661 PMCID: PMC8408985 DOI: 10.1186/s13073-021-00952-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/12/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Epithelial ovarian cancer (OC) is a heterogenous disease consisting of five major histologically distinct subtypes: high-grade serous (HGSOC), low-grade serous (LGSOC), endometrioid (ENOC), clear cell (CCOC) and mucinous (MOC). Although HGSOC is the most prevalent subtype, representing 70-80% of cases, a 2013 landmark study by Domcke et al. found that the most frequently used OC cell lines are not molecularly representative of this subtype. This raises the question, if not HGSOC, from which subtype do these cell lines derive? Indeed, non-HGSOC subtypes often respond poorly to chemotherapy; therefore, representative models are imperative for developing new targeted therapeutics. METHODS Non-negative matrix factorisation (NMF) was applied to transcriptomic data from 44 OC cell lines in the Cancer Cell Line Encyclopedia, assessing the quality of clustering into 2-10 groups. Epithelial OC subtypes were assigned to cell lines optimally clustered into five transcriptionally distinct classes, confirmed by integration with subtype-specific mutations. A transcriptional subtype classifier was then developed by trialling three machine learning algorithms using subtype-specific metagenes defined by NMF. The ability of classifiers to predict subtype was tested using RNA sequencing of a living biobank of patient-derived OC models. RESULTS Application of NMF optimally clustered the 44 cell lines into five transcriptionally distinct groups. Close inspection of orthogonal datasets revealed this five-cluster delineation corresponds to the five major OC subtypes. This NMF-based classification validates the Domcke et al. analysis, in identifying lines most representative of HGSOC, and additionally identifies models representing the four other subtypes. However, NMF of the cell lines into two clusters did not align with the dualistic model of OC and suggests this classification is an oversimplification. Subtype designation of patient-derived models by a random forest transcriptional classifier aligned with prior diagnosis in 76% of unambiguous cases. In cases where there was disagreement, this often indicated potential alternative diagnosis, supported by a review of histological, molecular and clinical features. CONCLUSIONS This robust classification informs the selection of the most appropriate models for all five histotypes. Following further refinement on larger training cohorts, the transcriptional classification may represent a useful tool to support the classification of new model systems of OC subtypes.
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Affiliation(s)
- Bethany M Barnes
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Louisa Nelson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Anthony Tighe
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Oxford Road, Manchester, M13 9WL, UK
| | - I-Hsuan Lin
- Bioinformatics Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
| | - Sudha Desai
- Department of Histopathology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Joanne C McGrail
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Robert D Morgan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK.
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Wang X, Cao A, Hou Z, Li X, Gao B. Identification of key classification features of early cervical squamous cell carcinoma. Comput Biol Chem 2021; 93:107531. [PMID: 34217008 DOI: 10.1016/j.compbiolchem.2021.107531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/11/2021] [Accepted: 06/16/2021] [Indexed: 11/23/2022]
Abstract
Despite the tremendous progress in molecular analysis of pan-cancer, little is known regarding molecular classification of cervical squamous cell carcinoma. In this study, we adopted a multi-omics approach to identify potential key classification features of cervical squamous cell carcinoma. Specifically, we analyzed mRNA, and microRNA (miRNA) expression data, as well as DNA methylation and copy number variation in cervical squamous cell carcinoma cases, using datasets obtained from The Cancer Genome Atlas (TCGA). Moreover, we identified molecules in each dimension, as well as integrated and clustered filtered classification features, and used them to distinguish different subtypes. The resulting key classification features were used to establish a classification model for cervical squamous cell carcinoma. Our results revealed two cervical squamous cell carcinoma subtypes, with significant differences across clinical survival levels, as well as 8 key classification features of cervical squamous cell carcinomas. These findings are expected to provide important references for early classification of cervical squamous cell carcinoma and identification of classification markers.
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Gao Y, Song F, Zhang P, Liu J, Cui J, Ma Y, Zhang G, Luo J. Improving the Subtype Classification of Non-small Cell Lung Cancer by Elastic Deformation Based Machine Learning. J Digit Imaging 2021; 34:605-617. [PMID: 33963422 PMCID: PMC8329138 DOI: 10.1007/s10278-021-00455-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/06/2021] [Accepted: 04/27/2021] [Indexed: 01/02/2023] Open
Abstract
Non-invasive image-based machine learning models have been used to classify subtypes of non-small cell lung cancer (NSCLC). However, the classification performance is limited by the dataset size, because insufficient data cannot fully represent the characteristics of the tumor lesions. In this work, a data augmentation method named elastic deformation is proposed to artificially enlarge the image dataset of NSCLC patients with two subtypes (squamous cell carcinoma and large cell carcinoma) of 3158 images. Elastic deformation effectively expanded the dataset by generating new images, in which tumor lesions go through elastic shape transformation. To evaluate the proposed method, two classification models were trained on the original and augmented dataset, respectively. Using augmented dataset for training significantly increased classification metrics including area under the curve (AUC) values of receiver operating characteristics (ROC) curves, accuracy, sensitivity, specificity, and f1-score, thus improved the NSCLC subtype classification performance. These results suggest that elastic deformation could be an effective data augmentation method for NSCLC tumor lesion images, and building classification models with the help of elastic deformation has the potential to serve for clinical lung cancer diagnosis and treatment design.
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Affiliation(s)
- Yang Gao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Fan Song
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, 100083, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Peng Zhang
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, 100083, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Jian Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, 100083, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Jingjing Cui
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, 100083, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Yingying Ma
- Medical Engineering Management Office, Shandong Provincial Hospital Affiliated To Shandong University, Jinan, 250021, China
| | - Guanglei Zhang
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, 100083, China.
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Jianwen Luo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China.
- Center for Biomedical Imaging Research, Tsinghua University, Beijing, China.
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Abstract
In this research, we exploit an image-based deep learning framework to distinguish three major subtypes of renal cell carcinoma (clear cell, papillary, and chromophobe) using images acquired with computed tomography (CT). A biopsy-proven benchmarking dataset was built from 169 renal cancer cases. In each case, images were acquired at three phases(phase 1, before injection of the contrast agent; phase 2, 1 min after the injection; phase 3, 5 min after the injection). After image acquisition, rectangular ROI (region of interest) in each phase image was marked by radiologists. After cropping the ROIs, a combination weight was multiplied to the three-phase ROI images and the linearly combined images were fed into a deep learning neural network after concatenation. A deep learning neural network was trained to classify the subtypes of renal cell carcinoma, using the drawn ROIs as inputs and the biopsy results as labels. The network showed about 0.85 accuracy, 0.64–0.98 sensitivity, 0.83–0.93 specificity, and 0.9 AUC. The proposed framework which is based on deep learning method and ROIs provided by radiologists showed promising results in renal cell subtype classification. We hope it will help future research on this subject and it can cooperate with radiologists in classifying the subtype of lesion in real clinical situation.
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Affiliation(s)
- Seokmin Han
- Korea National University of Transportation, Uiwang-si, Gyeonggi-do, South Korea
| | - Sung Il Hwang
- Department of Radiology, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, South Korea.
| | - Hak Jong Lee
- Department of Radiology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, South Korea.,Department of Nanoconvergence, Seoul National University Graduate School of Convergence Science and Technology, Suwon-si, Gyeonggi-do, South Korea
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Li YM, Ren Y, Chen T, Tian HM. [Update and Research Progress in the Diagnosis of Primary Aldosteronism]. Sichuan Da Xue Xue Bao Yi Xue Ban 2020; 51:267-277. [PMID: 32543129 DOI: 10.12182/20200560201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Primary aldosteronism (PA) is the most common cause of secondary hypertension. The diagnosis procedure of PA includes screening, confirmatory diagnosis and subtype classification. International and national guidelines recommended plasma aldosterone concentration (PAC) to plasma renin activity (PRA) ratio (ARR) to detect possible cases of PA, and one or more tests (fludrocortisone suppression test, saline infusion test, oral sodium loading test, or captopril challenge test) to confirm ARR positive patients. Adrenal venous sampling (AVS) is also recommended as the best method to distinguish unilateral and bilateral adrenal disease when surgical treatment is feasible and desired by the patient. However, many studies find that each of the above diagnostic method has shortcomings. Recently, more and more studies are attempting to explore new methods with higher diagnostic efficiency and more conveniences, including new screening tests, new confirmatory diagnostic tests, new imaging and pathological histology methods. In our studies, the regression model, which included upright PAC, upright PRA, and lowest potassium, is superior to ARR for PA screening; the blood potassium and the ratio of blood potassium to blood sodium after the saline infusion test are not suitable for PA subtyping. This article will review the advances and progress in PA diagnosis.
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Affiliation(s)
- Yuan-Mei Li
- Adrenal Center, Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu 610041, China.,Department of Endocrine and Metabolic Diseases, Suining Central Hospital, Suining 629000, China
| | - Yan Ren
- Adrenal Center, Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Chen
- Adrenal Center, Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao-Ming Tian
- Adrenal Center, Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu 610041, China
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Tomar AK, Agarwal R, Kundu B. Most Variable Genes and Transcription Factors in Acute Lymphoblastic Leukemia Patients. Interdiscip Sci 2019; 11:668-678. [PMID: 30972690 DOI: 10.1007/s12539-019-00325-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/21/2019] [Accepted: 02/26/2019] [Indexed: 12/28/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a hematologic tumor caused by cell cycle aberrations due to accumulating genetic disturbances in the expression of transcription factors (TFs), signaling oncogenes and tumor suppressors. Though survival rate in childhood ALL patients is increased up to 80% with recent medical advances, treatment of adults and childhood relapse cases still remains challenging. Here, we have performed bioinformatics analysis of 207 ALL patients' mRNA expression data retrieved from the ICGC data portal with an objective to mark out the decisive genes and pathways responsible for ALL pathogenesis and aggression. For analysis, 3361 most variable genes, including 276 transcription factors (out of 16,807 genes) were sorted based on the coefficient of variance. Silhouette width analysis classified 207 ALL patients into 6 subtypes and heat map analysis suggests a need of large and multicenter dataset for non-overlapping subtype classification. Overall, 265 GO terms and 32 KEGG pathways were enriched. The lists were dominated by cancer-associated entries and highlight crucial genes and pathways that can be targeted for designing more specific ALL therapeutics. Differential gene expression analysis identified upregulation of two important genes, JCHAIN and CRLF2 in dead patients' cohort suggesting their possible involvement in different clinical outcomes in ALL patients undergoing the same treatment.
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Affiliation(s)
- Anil Kumar Tomar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Rahul Agarwal
- Department of Reproductive Biology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
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Zhou M, Zhao H, Xu W, Bao S, Cheng L, Sun J. Discovery and validation of immune-associated long non-coding RNA biomarkers associated with clinically molecular subtype and prognosis in diffuse large B cell lymphoma. Mol Cancer 2017; 16:16. [PMID: 28103885 PMCID: PMC5248456 DOI: 10.1186/s12943-017-0580-4] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/03/2017] [Indexed: 01/18/2023] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is an aggressive and complex disease characterized by wide clinical, phenotypic and molecular heterogeneities. The expression pattern and clinical implication of long non-coding RNAs (lncRNAs) between germinal center B-cell-like (GCB) and activated B-cell-like (ABC) subtypes in DLBCL remain unclear. This study aims to determine whether lncRNA can serve as predictive biomarkers for subtype classification and prognosis in DLBCL. Methods Genome-wide comparative analysis of lncRNA expression profiles were performed in a large number of DLBCL patients from Gene Expression Omnibus (GEO), including GSE31312 cohort (N = 426), GSE10846 (N = 350) cohort and GSE4475 cohort (N = 129). Novel lncRNA biomarkers associated with clinically molecular subtype and prognosis were identified in the discovery cohort using differential expression analyses and weighted voting algorithm. The predictive value of the lncRNA signature was then assessed in two independent cohorts. The functional implication of lncRNA signature was also analyzed by integrative analysis of lncRNA and mRNA. Results Seventeen of the 156 differentially expressed lncRNAs between GCB and ABC subtypes were identified as candidate biomarkers and integrated into form a lncRNA-based signature (termed SubSigLnc-17) which was able to discriminate between GCB and ABC subtypes with AUC of 0.974, specificity of 89.6% and sensitivity of 92.5%. Furthermore, subgroups of patients characterized by the SubSigLnc-17 demonstrated significantly different clinical outcome. The reproducible predictive power of SubSigLnc-17 in subtype classification and prognosis was successfully validated in the internal validation cohort and another two independent patient cohorts. Integrative analysis of lncRNA-mRNA suggested that these candidate lncRNA biomarkers were mainly related to immune-associated processes, such as T cell activation, leukocyte activation, lymphocyte activation and Chemokine signaling pathway. Conclusions Our study uncovered differentiated lncRNA expression pattern between GCB and ABC DLBCL and identified a 17-lncRNA signature for subtype classification and prognosis prediction. With further prospective validation, our study will improve the understanding of underlying molecular heterogeneities in DLBCL and provide candidate lncRNA biomarkers in DLBCL classification and prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0580-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Hengqiang Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Wanying Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Siqi Bao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China.
| | - Jie Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China.
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Gendoo DM, Haibe-Kains B. MM2S: personalized diagnosis of medulloblastoma patients and model systems. Source Code Biol Med 2016; 11:6. [PMID: 27069505 DOI: 10.1186/s13029-016-0053-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/31/2016] [Indexed: 12/04/2022]
Abstract
Background Medulloblastoma (MB) is a highly malignant and heterogeneous brain tumour that is the most common cause of cancer-related deaths in children. Increasing availability of genomic data over the last decade had resulted in improvement of human subtype classification methods, and the parallel development of MB mouse models towards identification of subtype-specific disease origins and signaling pathways. Despite these advances, MB classification schemes remained inadequate for personalized prediction of MB subtypes for individual patient samples and across model systems. To address this issue, we developed the Medullo-Model to Subtypes (MM2S) classifier, a new method enabling classification of individual gene expression profiles from MB samples (patient samples, mouse models, and cell lines) against well-established molecular subtypes [Genomics 106:96-106, 2015]. We demonstrated the accuracy and flexibility of MM2S in the largest meta-analysis of human patients and mouse models to date. Here, we present a new functional package that provides an easy-to-use and fully documented implementation of the MM2S method, with additional functionalities that allow users to obtain graphical and tabular summaries of MB subtype predictions for single samples and across sample replicates. The flexibility of the MM2S package promotes incorporation of MB predictions into large Medulloblastoma-driven analysis pipelines, making this tool suitable for use by researchers. Results The MM2S package is applied in two case studies involving human primary patient samples, as well as sample replicates of the GTML mouse model. We highlight functions that are of use for species-specific MB classification, across individual samples and sample replicates. We emphasize on the range of functions that can be used to derive both singular and meta-centric views of MB predictions, across samples and across MB subtypes. Conclusions Our MM2S package can be used to generate predictions without having to rely on an external web server or additional sources. Our open-source package facilitates and extends the MM2S algorithm in diverse computational and bioinformatics contexts. The package is available on CRAN, at the following URL: https://cran.r-project.org/web/packages/MM2S/, as well as on Github at the following URLs: https://github.com/DGendoo and https://github.com/bhklab. Electronic supplementary material The online version of this article (doi:10.1186/s13029-016-0053-y) contains supplementary material, which is available to authorized users.
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Nanba K, Tsuiki M, Umakoshi H, Nanba A, Hirokawa Y, Usui T, Tagami T, Shimatsu A, Suzuki T, Tanabe A, Naruse M. Shortened saline infusion test for subtype prediction in primary aldosteronism. Endocrine 2015; 50:802-6. [PMID: 25931414 DOI: 10.1007/s12020-015-0615-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/21/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Kazutaka Nanba
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Mika Tsuiki
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Hironobu Umakoshi
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Aya Nanba
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Yuusuke Hirokawa
- Department of Radiology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Takeshi Usui
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Tetsuya Tagami
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Akira Shimatsu
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan
| | - Tomoko Suzuki
- Department of Public Health, Kitasato University School of Medicine, Kanagawa, Japan
| | - Akiyo Tanabe
- Department of Endocrinology, Metabolism, and Diabetes, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mitsuhide Naruse
- Department of Endocrinology, Metabolism, and Hypertension, National Hospital Organization Kyoto Medical Center, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto, 612-8555, Japan.
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Figueiredo AS, Lampe E, do Espírito-Santo MP, Mello FCDA, de Almeida FQ, de Lemos ERS, Godoi TLOS, Dimache LAG, Dos Santos DRL, Villar LM. Identification of two phylogenetic lineages of equine hepacivirus and high prevalence in Brazil. Vet J 2015; 206:414-6. [PMID: 26545848 DOI: 10.1016/j.tvjl.2015.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/11/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
Non-primate hepacivirus (NPHV), as described in horses, is the virus most genetically related to hepatitis C virus (HCV). Although detected worldwide, limited data on genomic variability and distribution of NPHV are available in Latin America. The aim of this study was to investigate the genetic diversity and prevalence of equine NPHV in Brazil. Thirteen percent of 202 equines from three Brazilian states were positive for NPHV genome by reverse transcriptase PCR. Nucleotide sequences of the partial NS5B genome presented the greatest diversity described to date (25.6%), which is comparable to the upper limit of diversity for HCV subtype classification for the same region. Phylogenetic analysis revealed that Brazilian NPHV sequences along with isolates worldwide form two strongly supported clades (pp = 1.0) suggesting the existence of two distinct lineages.
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Affiliation(s)
| | - Elisabeth Lampe
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, RJ, 21040-360 Brazil
| | | | | | - Fernando Queiroz de Almeida
- Veterinary Institute, Federal Rural University of Rio de Janeiro, UFRRJ, Rio de Janeiro, RJ 23851-970 Brazil
| | - Elba Regina Sampaio de Lemos
- Laboratory of Hantaviruses and Rickettsioses, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, RJ, 21040-360 Brazil
| | | | - Luana Avila Giorgia Dimache
- Animal Science Institute, Federal Rural University of Rio de Janeiro, UFRRJ, Rio de Janeiro, RJ, 23851-970 Brazil
| | - Debora Regina Lopes Dos Santos
- Department of Veterinary Microbiology and Immunology, Federal Rural University of Rio de Janeiro, UFRRJ, Rio de Janeiro, RJ, 23851-970 Brazil
| | - Livia Melo Villar
- Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, RJ, 21040-360 Brazil
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Inoue M, Takahashi S, Soeda H, Shimodaira H, Watanabe M, Miura K, Sasaki I, Kato S, Ishioka C. Gene-expression profiles correlate with the efficacy of anti-EGFR therapy and chemotherapy for colorectal cancer. Int J Clin Oncol 2015; 20:1147-55. [PMID: 25990448 DOI: 10.1007/s10147-015-0841-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Comprehensive gene-expression analysis is very useful for classifying specific cancers into subgroups on the basis of their biological characteristics; it is used both prognostically and predictively. The purpose of this study was to classify unresectable advanced or recurrent colorectal cancer (CRC) by gene-expression profiling of formalin-fixed paraffin-embedded tissues and to correlate CRC subgroups with clinicopathological and molecular features and clinical outcomes. METHODS One hundred patients with advanced or recurrent CRC were enrolled. RNA extracted from FFPE tissues was subjected to gene-expression microarray analysis. RESULTS The patients were stratified into four subgroups (subtypes A1, A2, B1, and B2) by unsupervised hierarchical clustering. By use of principle-components analysis (PCA), the patients were divided into subtypes A and B on the basis of component 1 and into subtypes 1 and 2 on the basis of component 2. Subtype A was significantly enriched among patients without the KRAS mutation and with an earlier clinical stage at diagnosis. With regard to anti-EGFR therapy, progression-free survival (PFS) was better for patients in subtype A without the KRAS mutation than for those with the KRAS mutation (P = 0.047). PFS for patients without the KRAS mutation in subtype B was comparable with that for patients with the KRAS mutation (P = 0.55). Similar results were observed in a validation set. CONCLUSION We found that gene-expression profiles enabled stratification of CRC patients into four subgroups. The efficacy of anti-EGFR therapy was correlated with component 1 from PCA. This comprehensive study may explain the heterogeneity of unresectable advanced or recurrent CRC and could be useful for identifying novel biomarkers for CRC treatment.
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Affiliation(s)
- Masahiro Inoue
- Department of Clinical Oncology, Institute of Development, Aging and Cancer Tohoku University, 4-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan.,Department of Clinical Oncology, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Shin Takahashi
- Department of Clinical Oncology, Institute of Development, Aging and Cancer Tohoku University, 4-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan.,Department of Clinical Oncology, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Hiroshi Soeda
- Department of Clinical Oncology, Institute of Development, Aging and Cancer Tohoku University, 4-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan.,Department of Clinical Oncology, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Hideki Shimodaira
- Department of Clinical Oncology, Institute of Development, Aging and Cancer Tohoku University, 4-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan.,Department of Clinical Oncology, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Mika Watanabe
- Department of Pathology, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Koh Miura
- Department of Gastroenterological Surgery, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Iwao Sasaki
- Department of Gastroenterological Surgery, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Shunsuke Kato
- Department of Clinical Oncology, Institute of Development, Aging and Cancer Tohoku University, 4-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan.,Department of Clinical Oncology, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Institute of Development, Aging and Cancer Tohoku University, 4-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan. .,Department of Clinical Oncology, Tohoku University Hospital, 1-1 Seiryo-machi, Aobaku, Sendai, 980-8575, Japan.
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Yang WZ, Hu Y, Wu WY, Ye M, Guo DA. Saponins in the genus Panax L. (Araliaceae): a systematic review of their chemical diversity. Phytochemistry 2014; 106:7-24. [PMID: 25108743 DOI: 10.1016/j.phytochem.2014.07.012] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 05/04/2023]
Abstract
The Panax genus is a crucial source of natural medicines that has benefited human health for a long time. Three valuable medicinal herbs, namely Panax ginseng, Panax quinquefolius, and Panax notoginseng, have received considerable interest due to their extensive application in clinical therapy, healthcare products, and as foods and food additives world-wide. Panax species are known to contain abundant levels of saponins, also dubbed ginsenosides, which refer to a series of dammarane or oleanane type triterpenoid glycosides. These saponins exhibit modulatory effects to the central nervous system and beneficial effects to patients suffering from cardiovascular diseases, and also have anti-diabetic and anti-tumor properties. To the end of 2012, at least 289 saponins were reported from eleven different Panax species. This comprehensive review describes the advances in the phytochemistry of the genus Panax for the period 1963-2012, based on the 134 cited references. The reported saponins can be classified into protopanaxadiol, protopanaxatriol, octillol, oleanolic acid, C17 side-chain varied, and miscellaneous subtypes, according to structural differences in sapogenins. The investigational history of Panax is also reviewed, with special attention being paid to the structural features of the six different subtypes, together with their (1)H and (13)C NMR spectroscopic characteristics which are useful for determining their structures and absolute configuration.
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Affiliation(s)
- Wen-Zhi Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Ying Hu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Wan-Ying Wu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China.
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China.
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