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Gao Y, Wu C, Huang J, Huang Z, Jin Z, Guo S, Tao X, Lu S, Zhang J, Zhang F, Zhai Y, Shi R, Ye P, Wu J. A new strategy to identify ADAM12 and PDGFRB as a novel prognostic biomarker for matrine regulates gastric cancer via high throughput chip mining and computational verification. Comput Biol Med 2023; 166:107562. [PMID: 37847945 DOI: 10.1016/j.compbiomed.2023.107562] [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: 07/28/2023] [Revised: 08/26/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Gastric cancer is a life-threatening disease that poses a serious risk to human health. Although there are numerous molecular targets for gastric cancer in clinical practice, they often exhibit low specificity and sensitivity. Consequently, this can result in a low early diagnosis rate, delayed treatment, and poor prognosis for patients with gastric cancer. Hence, it remains crucial to identify more precise diagnostic markers for this disease. METHODS This study utilized ceRNA chips and bioinformatics methods to investigate the key genes and mechanisms involved in matrine intervention in gastric cancer cells. RESULTS ADAM12 and PDGFRB are the key genes that are down-regulated after matrine intervention in gastric cancer cells. By conducting bioinformatics analysis, two ceRNA regulatory axes were identified, which are associated with the prognosis of gastric cancer. These axes are lncRNA DGCR5/hsa-miR-206/ADAM12 and circRNA ITGA3/hsa-miR-24-3p/PDGFRB. CONCLUSION The low expression of ADAM12 may weaken the digestion of extracellular matrix (ECM) molecules, which can result in the invasion and metastasis of tumor cells. This occurs without the catalysis of ECM proteases, thereby impacting the invasion and metastasis of gastric cancer cells. Additionally, the analysis of immune infiltration suggests that ADAM12 and PDGFRB may influence changes in the tumor immune microenvironment, thereby affecting the occurrence and development of gastric cancer. This study contributes to a deeper understanding of the role of the matrine-related ceRNA network in gastric cancer, providing a reference for clinical diagnosis and treatment. It holds significant importance in discovering new drug treatment targets.
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Affiliation(s)
- Yifei Gao
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chao Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jiaqi Huang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhihong Huang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhengsen Jin
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Siyu Guo
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaoyu Tao
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shan Lu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jingyuan Zhang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Fanqin Zhang
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yiyan Zhai
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Rui Shi
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Peizhi Ye
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jiarui Wu
- Department of Clinical Pharmacology of Traditional Chinese Medicine, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Huang J, Zhang J, Zhang F, Lu S, Guo S, Shi R, Zhai Y, Gao Y, Tao X, Jin Z, You L, Wu J. Identification of a disulfidptosis-related genes signature for prognostic implication in lung adenocarcinoma. Comput Biol Med 2023; 165:107402. [PMID: 37657358 DOI: 10.1016/j.compbiomed.2023.107402] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 06/29/2023] [Revised: 07/24/2023] [Accepted: 08/26/2023] [Indexed: 09/03/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most prevalent subtype of non-small cell lung cancer. Additionally, disulfidptosis, a newly discovered type of cell death, has been found to be closely associated with the onset and progression of tumors. METHODS The study first identified genes related to disulfidptosis through correlation analysis. These genes were then screened using univariate cox regression and LASSO regression, and a prognostic model was constructed through multivariate cox regression. A nomogram was also created to predict the prognosis of LUAD. The model was validated in three independent data sets: GSE72094, GSE31210, and GSE37745. Next, patients were grouped based on their median risk score, and differentially expressed genes between the two groups were analyzed. Enrichment analysis, immune infiltration analysis, and drug sensitivity evaluation were also conducted. RESULTS In this study, we examined 21 genes related to disulfidptosis and developed a gene signature that was found to be associated with a poorer prognosis in LUAD. Our model was validated using three independent datasets and showed AUC values greater than 0.5 at 1, 3, and 5 years. Enrichment analysis revealed that the disulfidptosis-related genes signature had a multifaceted impact on LUAD, particularly in relation to tumor development, proliferation, and metastasis. Patients in the high-risk group exhibited higher tumor purity and lower stromal score, ESTIMATE score, and Immune score. CONCLUSION This study constructed a gene signature related to disulfidptosis in lung adenocarcinoma and analyzed its impact on the disease and its association with the tumor microenvironment. The findings of this research provide valuable insights into the understanding of lung adenocarcinoma and could potentially lead to the development of new treatment strategies.
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Affiliation(s)
- Jiaqi Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jingyuan Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Fanqin Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Shan Lu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Siyu Guo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Rui Shi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yiyan Zhai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yifei Gao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaoyu Tao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhengsen Jin
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Leiming You
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jiarui Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Chicco D, Sanavia T, Jurman G. Signature literature review reveals AHCY, DPYSL3, and NME1 as the most recurrent prognostic genes for neuroblastoma. BioData Min 2023; 16:7. [PMID: 36870971 PMCID: PMC9985261 DOI: 10.1186/s13040-023-00325-1] [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: 09/19/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Neuroblastoma is a childhood neurological tumor which affects hundreds of thousands of children worldwide, and information about its prognosis can be pivotal for patients, their families, and clinicians. One of the main goals in the related bioinformatics analyses is to provide stable genetic signatures able to include genes whose expression levels can be effective to predict the prognosis of the patients. In this study, we collected the prognostic signatures for neuroblastoma published in the biomedical literature, and noticed that the most frequent genes present among them were three: AHCY, DPYLS3, and NME1. We therefore investigated the prognostic power of these three genes by performing a survival analysis and a binary classification on multiple gene expression datasets of different groups of patients diagnosed with neuroblastoma. Finally, we discussed the main studies in the literature associating these three genes with neuroblastoma. Our results, in each of these three steps of validation, confirm the prognostic capability of AHCY, DPYLS3, and NME1, and highlight their key role in neuroblastoma prognosis. Our results can have an impact on neuroblastoma genetics research: biologists and medical researchers can pay more attention to the regulation and expression of these three genes in patients having neuroblastoma, and therefore can develop better cures and treatments which can save patients' lives.
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Affiliation(s)
- Davide Chicco
- Institute of Health Policy Management and Evaluation, University of Toronto, 155 College Street, M5T 3M7 Toronto, Ontario, Canada
| | - Tiziana Sanavia
- Dipartimento di Scienze Mediche, Università di Torino, Via Verdi 8, 10124 Turin, Italy
| | - Giuseppe Jurman
- Data Science for Health Unit, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo (Trento), Italy
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Swami N, Nguyen T, Ogobuiro I, Abramowitz M, Chipidza F, Davicioni E, Meiyappan K, Pra AD, Nguyen PL, Pollack A, Punnen S, Mahal BA, Alshalalfa M. Distinct Profiles of DNA Repair Activity Define Favorable-risk Prostate Cancer Subtypes With Divergent Outcome. Clin Genitourin Cancer 2023; 21:76-83. [PMID: 36522269 DOI: 10.1016/j.clgc.2022.11.005] [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: 09/01/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Understanding if divergent molecular profiles of DNA damage and repair (DDR) pathway activity, a biomarker of disease progression, exist in prostate tumors with favorable-risk features is an unmet need, which this study aim to unearth. MATERIALS AND METHODS This was a multicenter registry genome-wide expression profiling study of prospectively collected radical prostatectomy (RP) tumor samples from 2014 to 2016. DDR activity was calculated from average expression of 372 DDR genes. Consensus hierarchical clustering was used to arrive at a robust clustering solution based on DDR gene expression patterns. Genome-wide differential expression between clusters was performed, and outcomes were evaluated across expression patterns. RESULTS Of 5239 patients from the prospective registry, 376 had favorable-risk disease (Grade group [GG] 1 to 2, PSA prior to RP <10ng/ml, pT2 or less). DDR activity score was correlated with prognostic genomic signatures that predict for metastatic risk (r = 0.37, P < 2e-16) and high grade groups (P < .001). High DDR activity (top-quartile) was observed in 28% of patients with favorable-risk disease. In favorable-risk disease, 3 distinct clusters with varied DDR activity emerged with consensus clustering. Cluster I (compared with cluster II-III and GG3-GG5 disease) had the highest expression of all DDR sub-pathways, MYC, PAPR1, AR, and AR activity (P < .001 for all). Furthermore, cluster I was associated with poorer metastasis-free survival (MFS) and Overall survival (OS) compared with other clusters (MFS; HR: 2.43, 95%CI, [1.22-4.83], P = .01; OS; HR: 2.77, 95%CI, [1.18-6.5], P = .01). CONCLUSIONS Cluster I is a novel subgroup of favorable-risk disease with high DDR activity, AR activity, PARP1 and chr8q/MYC expression, and poorer MFS and OS.
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Affiliation(s)
- Nishwant Swami
- University of Massachusetts Medical School, Worcester, MA
| | - Tiffany Nguyen
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Ifeanyichukwu Ogobuiro
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Matthew Abramowitz
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Fallon Chipidza
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | | | - Karthik Meiyappan
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Alan Dal Pra
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Paul L Nguyen
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA
| | - Alan Pollack
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Sanoj Punnen
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Brandon A Mahal
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Mohammed Alshalalfa
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL.
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Hao K, Li J, Zhang Y, Zhao W, Chen X, Xu J, Tian Y, Li X, Fen J, He X. Expression and prognostic signatures of m6A-related lncRNAs in hepatocellular carcinoma. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04338-x. [PMID: 36121511 DOI: 10.1007/s00432-022-04338-x] [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: 07/27/2022] [Accepted: 08/29/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND N6-methyladenosine (m6A) is a common modification and plays an important role in various biological processes, but m6A-related lncRNA functions in hepatocellular carcinoma (HCC) have not been systematically clarified. METHODS The clinical data and RNA-seq transcriptome of 375 cases of HCC and 50 cases of normal tissues were obtained from the Cancer Gene Atlas database. Co-expression analysis was used to obtain m6A-related lncRNA. The independent prognostic factors were identified by univariate and multivariate Cox regression models. Kaplan-Meier method was used in survival analysis. The core gene of the mRNA-mRNA interaction network is related to m6A-related lncRNAs obtained by the CytoHubba plugin of Cytoscape. Gene ontology and Kyoto Gene Encyclopedia were analyzed to find out the potential mechanism. CIBERSORT algorithm was used to calculate the relative proportion of immune infiltrating cells. RESULTS We identified two subgroups (cluster 1 and cluster 2) according to the expression level. The survival analysis curve and receiver operating characteristic curve proved that this model could predict the prognosis of HCC patients. The univariate and multivariate Cox regression analyses showed the independent prognostic value. UBE2C was screened as the pivotal gene. The expression level of m6A-related lncRNAs causes changes in the tumor immune microenvironment. CONCLUSION The expression levels of m6A-related lncRNAs were significantly different and the prognostic value of m6A-related lncRNAs was confirmed. The m6A-related lncRNAs are expected to be prognostic signatures in HCC.
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Affiliation(s)
- Kenan Hao
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jincheng Li
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.,Radiology Department, Guangdong Second Provincial Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Youao Zhang
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Wei Zhao
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xiaojing Chen
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jiabin Xu
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Ye Tian
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xinmin Li
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Jianyu Fen
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China
| | - Xiaofeng He
- Division of Vascular and Interventional Radiology, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
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6
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Nie X, Tan J. N6-methyladenosine-related lncRNAs is a potential marker for predicting prognosis and immunotherapy in ovarian cancer. Hereditas 2022; 159:17. [PMID: 35303965 PMCID: PMC8933961 DOI: 10.1186/s41065-022-00222-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 12/02/2022] Open
Abstract
Background With a lack of specific symptoms, ovarian cancer (OV) is often diagnosed at an advanced stage. This coupled with inadequate prognostic indicators and treatments with limited therapeutic effect make OV the deadliest type of gynecological tumor. Recent research indicates that N6-methyladenosine (m6A) and long-chain non-coding RNA (lncRNA) play important roles in the prognosis of OV and the efficacy of immunotherapy. Results Using the Cancer Genome Atlas (TCGA) OV-related data set and the expression profiles of 21 m6A-related genes, we identified two m6A subtypes, and the differentially expressed genes between the two. Based on the differentially expressed lncRNAs in the two m6A subtypes and the lncRNAs co-expressed with the 21 m6A-related genes, single-factor cox and LASSO regression were used to further isolate the 13 major lncRNAs. Finally, multi-factor cox regression was used to construct a m6A-related lncRNA risk score model for OV, with good performance in patient prognosis. Using risk score, OV tumor samples are divided into with high- and low-score groups. We explored the differences in clinical characteristics, tumor mutational burden, and tumor immune cell infiltration between the two groups, and evaluated the risk score’s ability to predict the benefit of immunotherapy. Conclusion Our m6A-based lncRNA risk model could be used to predict the prognosis and immunotherapy response of future OV patients. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00222-3.
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Affiliation(s)
- Xin Nie
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, China
| | - Jichun Tan
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China. .,Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, China.
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7
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Miao D, Shi J, Xiong Z, Xiao W, Meng X, Lv Q, Xie K, Yang H, Zhang X. As a prognostic biomarker of clear cell renal cell carcinoma RUFY4 predicts immunotherapy responsiveness in a PDL1-related manner. Cancer Cell Int 2022; 22:66. [PMID: 35135552 PMCID: PMC8822671 DOI: 10.1186/s12935-022-02480-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/13/2021] [Accepted: 01/21/2022] [Indexed: 12/28/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most lethal malignancies in the urinary system and the existing immunotherapy has not achieved satisfactory outcomes. Therefore, this study aims at establishing a novel gene signature for immune infiltration and clinical outcome (overall survival and immunotherapy responsiveness) in ccRCC patients. Methods Based on RNA sequencing data and clinical information in The Cancer Genome Atlas (TCGA) database, we calculated proportions of immune cells in 611 samples using an online tool CIBERSORTx. Multivariate survival analysis was conducted to determine crucial survival-associated immune cells and immune-infiltration-related genes (IIRGs). Next, the clinical specimens and common renal cancer cell lines were applied to confirm IIRGs expression at protein and RNA levels. Finally, functional enrichment analyses and siRNA technology targeted to RUFY4 were implemented to verify its function of predicting immunotherapy response. Results Follicular helper T cells (TFHs) and Regulatory T cells (Tregs) were highly infiltrated in the tumor microenvironment (TME) and their relative proportions were independent prognostic factors for patients. Among IIRGs of TFHs and TREGs, RUFY4 was found to be highly activated in tumor microenvironment and its co-expression network was enriched in PDL1/PD1 checkpoint pathway in cancer. Additionally, knockdown of RUFY4 led to the decline of PDL1 and proliferation ability in ccRCC cell lines. Conclusion TFHs and Tregs were considered as prognostic biomarkers and RUFY4 was an immunotherapeutic predictor of ccRCC patients in a PDL1-Related manner. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02480-7.
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Affiliation(s)
- Daojia Miao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jian Shi
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wen Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiangui Meng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Qingyang Lv
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Kairu Xie
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hongmei Yang
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China. .,Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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8
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Dinh P, Graham JD, Elder EN, Kabir M, Doan TB, French J, Meybodi F, Hui R, Wilcken NR, Harnett PR, Hsu J, Stuart KE, Wang T, Ahern V, Brennan M, Fox SB, Dear RF, Lim E, White M, Mann GB, Pathmanathan N. Impact of the EndoPredict genomic assay on treatment decisions for oestrogen receptor-positive early breast cancer patients: benefits of physician selective testing. Breast Cancer Res Treat 2021; 191:501-511. [PMID: 34853987 DOI: 10.1007/s10549-021-06456-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/14/2021] [Indexed: 01/26/2023]
Abstract
PURPOSE Genomic tests improve accuracy of risk prediction for early breast cancers but these are expensive. This study evaluated the clinical utility of EndoPredict®, in terms of impact on adjuvant therapy recommendations and identification of parameters to guide selective application. METHODS Patients with ER-positive, HER2-negative, and early-stage invasive breast cancer were tested with EndoPredict®. Two cohorts were recruited: one consecutively and another at clinical team discretion. Systemic treatment recommendations were recorded before and after EndoPredict® results were revealed to the multidisciplinary team. RESULTS 233 patients were recruited across five sites: 123 consecutive and 110 at clinical team discretion. In the consecutive cohort 50.6% (62/123) cases were classified high risk of recurrence by EndoPredict®, compared with 62.7% (69/110) in the selective cohort. A change in treatment recommendation was significantly more likely (p < 0.0001) in the selective cohort (43/110, 39.1%) compared to the consecutive group (11/123, 8.9%). The strongest driver of selective recruitment was intermediate grade histology, whilst logistic regression modelling demonstrated that nodal status (p < 0.001), proliferative rate (p = 0.001), and progesterone receptor positivity (p < 0.001) were the strongest discriminators of risk. CONCLUSION Whilst molecular risk can be predicted by traditional variables in a high proportion of cases, EndoPredict® had a greater impact on treatment decisions in those cases selected for testing at team discretion. This is indicative of the robust ability of the clinical team to identify cases most likely to benefit from testing, underscoring the value of genomic tests in the oncologists' tool kit.
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Affiliation(s)
- Phuong Dinh
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - J Dinny Graham
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Elisabeth N Elder
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Masrura Kabir
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia
| | - Tram B Doan
- The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, 2145, Australia
| | - James French
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Farid Meybodi
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Rina Hui
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Nicholas R Wilcken
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Paul R Harnett
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Jeremy Hsu
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Kirsty E Stuart
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Tim Wang
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia.,Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Verity Ahern
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Meagan Brennan
- Crown Princess Mary Cancer Centre, Western Sydney Local Health District, Westmead, NSW, 2145, Australia.,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Rachel F Dear
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia
| | - Elgene Lim
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia.,Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | | | - G Bruce Mann
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Royal Melbourne Hospital, Parkville, VIC, 3050, Australia
| | - Nirmala Pathmanathan
- Westmead Breast Cancer Institute, Westmead, NSW, 2145, Australia. .,Westmead Clinical School, University of Sydney, Westmead, NSW, 2145, Australia. .,Douglass Hanly Moir Pathology, Macquarie Park, NSW, 2113, Australia.
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9
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Haynes BP, Schuster G, Buus R, Alataki A, Ginsburg O, Quang LH, Han PT, Khoa PH, Van Dinh N, Van To T, Clemons M, Holcombe C, Osborne C, Evans A, Skene A, Sibbering M, Rogers C, Laws S, Noor L, Cheang MCU, Cleator SJ, Smith IE, Dowsett M. Impact of the menstrual cycle on commercial prognostic gene signatures in oestrogen receptor-positive primary breast cancer. Breast Cancer Res Treat 2021; 190:295-305. [PMID: 34524591 PMCID: PMC8558287 DOI: 10.1007/s10549-021-06377-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022]
Abstract
PURPOSE Changes occur in the expression of oestrogen-regulated and proliferation-associated genes in oestrogen receptor (ER)-positive breast tumours during the menstrual cycle. We investigated if Oncotype® DX recurrence score (RS), Prosigna® (ROR) and EndoPredict® (EP/EPclin) prognostic tests, which include some of these genes, vary according to the time in the menstrual cycle when they are measured. METHODS Pairs of test scores were derived from 30 ER-positive/human epidermal growth factor receptor-2-negative tumours sampled at two different points of the menstrual cycle. Menstrual cycle windows were prospectively defined as either W1 (days 1-6 and 27-35; low oestrogen and low progesterone) or W2 (days 7-26; high oestrogen and high or low progesterone). RESULTS The invasion module score of RS was lower (- 10.9%; p = 0.098), whereas the ER (+ 16.6%; p = 0.046) and proliferation (+ 7.3%; p = 0.13) module scores were higher in W2. PGR expression was significantly increased in W2 (+ 81.4%; p = 0.0029). Despite this, mean scores were not significantly different between W1 and W2 for any of the tests and the two measurements showed high correlation (r = 0.72-0.93). However, variability between the two measurements led to tumours being assigned to different risk categories in the following proportion of cases: RS 22.7%, ROR 27.3%, EP 13.6% and EPclin 13.6%. CONCLUSION There are significant changes during the menstrual cycle in the expression of some of the genes and gene module scores comprising the RS, ROR and EP/EPclin scores. These did not affect any of the prognostic scores in a systematic fashion, but there was substantial variability in paired measurements.
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Affiliation(s)
- Ben P Haynes
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, UK
| | - Gene Schuster
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Richard Buus
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Anastasia Alataki
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK
| | - Ophira Ginsburg
- Department of Medicine, University of Toronto, Toronto, Canada
- Department of Population Health, Perlmutter Cancer Center, NYU Langone Health, New York, USA
| | - Le Hong Quang
- Department of Breast Surgery, National Cancer Hospital, Hanoi, Vietnam
| | - Pham Thi Han
- Department of Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Pham Hong Khoa
- Department of Breast Surgery, National Cancer Hospital, Hanoi, Vietnam
| | - Nguyen Van Dinh
- Department of Breast Surgery, National Cancer Hospital, Hanoi, Vietnam
| | - Ta Van To
- Department of Pathology, National Cancer Hospital, Hanoi, Vietnam
| | - Mark Clemons
- Division of Medical Oncology, Department of Medicine, The Ottawa Hospital and University of Ottawa, Ottawa, Canada
| | - Chris Holcombe
- Royal Liverpool University Hospital, Prescott Street, Liverpool, UK
| | | | | | - Anthony Skene
- Royal Bournemouth Hospital, Castle Lane East, Bournemouth, Dorset, UK
| | | | - Clare Rogers
- Doncaster Royal Infirmary, Armthorpe Road, Doncaster, South Yorkshire, UK
| | - Siobhan Laws
- Royal Hampshire County Hospital, Winchester, Hampshire, UK
| | - Lubna Noor
- University Hospital North Tees, Hardwick Road, Stockton-on-Tees, UK
| | | | - Susan J Cleator
- Department of Clinical Oncology, Imperial Healthcare NHS Trust, London, UK
| | - Ian E Smith
- The Breast Unit, Department of Medicine, Royal Marsden Hospital, Fulham Road, London, UK
| | - Mitch Dowsett
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK.
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10
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Herrera M, Berral-González A, López-Cade I, Galindo-Pumariño C, Bueno-Fortes S, Martín-Merino M, Carrato A, Ocaña A, De La Pinta C, López-Alfonso A, Peña C, García-Barberán V, De Las Rivas J. Cancer-associated fibroblast-derived gene signatures determine prognosis in colon cancer patients. Mol Cancer 2021; 20:73. [PMID: 33926453 PMCID: PMC8082938 DOI: 10.1186/s12943-021-01367-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022] Open
Affiliation(s)
- Mercedes Herrera
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Alberto Berral-González
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca, Spain
| | - Igor López-Cade
- Molecular Oncology Laboratory, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Cristina Galindo-Pumariño
- Medical Oncology Department, Ramón y Cajal University Hospital, IRYCIS, CIBERONC, Alcalá University, Madrid, Spain
| | - Santiago Bueno-Fortes
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca, Spain
| | - Manuel Martín-Merino
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca, Spain.,Facultad de Informática, Universidad Pontificia de Salamanca (UPSA), Salamanca, Spain
| | - Alfredo Carrato
- Medical Oncology Department, Ramón y Cajal University Hospital, IRYCIS, CIBERONC, Alcalá University, Madrid, Spain
| | - Alberto Ocaña
- Experimental Therapeutics Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC) and CIBERONC, Madrid, Spain
| | - Carolina De La Pinta
- Radio-Oncology Department, Ramón y Cajal University Hospital, IRYCIS, Alcalá University, Madrid, Spain
| | | | - Cristina Peña
- Medical Oncology Department, Ramón y Cajal University Hospital, IRYCIS, CIBERONC, Alcalá University, Madrid, Spain.
| | - Vanesa García-Barberán
- Molecular Oncology Laboratory, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain.
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Salamanca, Spain.
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11
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Sofopoulos M, Fortis SP, Vaxevanis CK, Sotiriadou NN, Arnogiannaki N, Ardavanis A, Vlachodimitropoulos D, Perez SA, Baxevanis CN. The prognostic significance of peritumoral tertiary lymphoid structures in breast cancer. Cancer Immunol Immunother 2019; 68:1733-1745. [PMID: 31598757 DOI: 10.1007/s00262-019-02407-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 05/29/2019] [Accepted: 09/29/2019] [Indexed: 12/31/2022]
Abstract
Tumors and their surrounding area represent spatially organized "ecosystems", where tumor cells and the immune contextures of the different compartments are in a dynamic interplay, with potential clinical impact. Here, we aimed to investigate the prognostic significance of peritumoral tertiary lymphoid structures (TLS) either alone or jointly with the intratumoral densities and spatial distribution of CD8 + and CD163 + cells in breast cancer (BCa) patients. TLS were identified peritumorally, within the area distancing up to 5 mm from the infiltrative tumor border, counted and further characterized as adjacent or distal, in formalin-fixed, paraffin-embedded tumor tissue samples from a cohort of 167 patients, with histologically confirmed invasive ductal BCa. TLS and tumor-infiltrating immune cells were determined by H&E and immunohistochemistry. Clinical follow-up was available for 112 of these patients. Patients with peritumoral TLS exhibited worse disease-free survival (DFS) and overall survival (OS) as compared to patients lacking TLS. Moreover, the density of peritumoral TLS was found to be crucial for prognosis, since patients with abundant TLS exhibited the worst DFS and OS. By combining the density of adjacent TLS (aTLS) with our recently published intratumoral signatures based on the differential distribution of CD8 + and CD163 + in the tumor center and invasive margin, we created two improved immune signatures with superior prognostic strength and higher patient population coverage. Our observations strengthen the notion for the fundamental role of the dynamic interplay between the immune cells within the tumor microenvironment (center/invasive margin) and the tumor surrounding area (peritumoral TLS) on the clinical outcome of BCa patients.
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Affiliation(s)
| | - Sotirios P Fortis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 171 Alexandras Avenue, 11522, Athens, Greece
| | - Christoforos K Vaxevanis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 171 Alexandras Avenue, 11522, Athens, Greece
| | | | | | | | | | - Sonia A Perez
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 171 Alexandras Avenue, 11522, Athens, Greece
| | - Constantin N Baxevanis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 171 Alexandras Avenue, 11522, Athens, Greece.
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12
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Pece S, Disalvatore D, Tosoni D, Vecchi M, Confalonieri S, Bertalot G, Viale G, Colleoni M, Veronesi P, Galimberti V, Di Fiore PP. Identification and clinical validation of a multigene assay that interrogates the biology of cancer stem cells and predicts metastasis in breast cancer: A retrospective consecutive study. EBioMedicine 2019; 42:352-62. [PMID: 30846393 DOI: 10.1016/j.ebiom.2019.02.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/18/2019] [Indexed: 11/23/2022] Open
Abstract
Background Breast cancers show variations in the number and biological aggressiveness of cancer stem cells that correlate with their clinico-prognostic and molecular heterogeneity. Thus, prognostic stratification of breast cancers based on cancer stem cells might help guide patient management. Methods We derived a 20-gene stem cell signature from the transcriptional profile of normal mammary stem cells, capable of identifying breast cancers with a homogeneous profile and poor prognosis in in silico analyses. The clinical value of this signature was assessed in a prospective-retrospective cohort of 2, 453 breast cancer patients. Models for predicting individual risk of metastasis were developed from expression data of the 20 genes in patients randomly assigned to a training set, using the ridge-penalized Cox regression, and tested in an independent validation set. Findings Analyses revealed that the 20-gene stem cell signature provided prognostic information in Triple-Negative and Luminal breast cancer patients, independently of standard clinicopathological parameters. Through functional studies in individual tumours, we correlated the risk score assigned by the signature with the proliferative and self-renewal potential of the cancer stem cell population. By retraining the 20-gene signature in Luminal patients, we derived the risk model, StemPrintER, which predicted early and late recurrence independently of standard prognostic factors. Interpretation Our findings indicate that the 20-gene stem cell signature, by its unique ability to interrogate the biology of cancer stem cells of the primary tumour, provides a reliable estimate of metastatic risk in Triple-Negative and Luminal breast cancer patients independently of standard clinicopathological parameters.
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