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Nair MG, Mavatkar AD, Naidu CM, V. P. S, C. E. A, Rajarajan S, Sahoo S, Mohan G, Jaikumar VS, Ramesh RS, B. S. S, Jolly MK, Maliekal TT, Prabhu JS. Elucidating the Role of MicroRNA-18a in Propelling a Hybrid Epithelial-Mesenchymal Phenotype and Driving Malignant Progression in ER-Negative Breast Cancer. Cells 2024; 13:821. [PMID: 38786043 PMCID: PMC11119613 DOI: 10.3390/cells13100821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Epigenetic alterations that lead to differential expression of microRNAs (miRNAs/miR) are known to regulate tumour cell states, epithelial-mesenchymal transition (EMT) and the progression to metastasis in breast cancer. This study explores the key contribution of miRNA-18a in mediating a hybrid E/M cell state that is pivotal to the malignant transformation and tumour progression in the aggressive ER-negative subtype of breast cancer. The expression status and associated effects of miR-18a were evaluated in patient-derived breast tumour samples in combination with gene expression data from public datasets, and further validated in in vitro and in vivo breast cancer model systems. The clinical relevance of the study findings was corroborated against human breast tumour specimens (n = 446 patients). The down-regulated expression of miR-18a observed in ER-negative tumours was found to drive the enrichment of hybrid epithelial/mesenchymal (E/M) cells with luminal attributes, enhanced traits of migration, stemness, drug-resistance and immunosuppression. Further analysis of the miR-18a targets highlighted possible hypoxia-inducible factor 1-alpha (HIF-1α)-mediated signalling in these tumours. This is a foremost report that validates the dual role of miR-18a in breast cancer that is subtype-specific based on hormone receptor expression. The study also features a novel association of low miR-18a levels and subsequent enrichment of hybrid E/M cells, increased migration and stemness in a subgroup of ER-negative tumours that may be attributed to HIF-1α mediated signalling. The results highlight the possibility of stratifying the ER-negative disease into clinically relevant groups by analysing miRNA signatures.
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Affiliation(s)
- Madhumathy G. Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Apoorva D. Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Chandrakala M. Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Snijesh V. P.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Anupama C. E.
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Savitha Rajarajan
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
| | - Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science (Bangalore), Bengaluru 560012, Karnataka, India
| | - Gayathri Mohan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Vishnu Sunil Jaikumar
- Animal Research Facility, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Rakesh S. Ramesh
- Department of Surgical Oncology, St. John’s Medical College and Hospital, Bangalore 560034, Karnataka, India
| | - Srinath B. S.
- Department of Surgical Oncology, Sri Shankara Cancer Hospital and Research Centre, Bangalore 560004, Karnataka, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science (Bangalore), Bengaluru 560012, Karnataka, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram 695014, Kerala, India
| | - Jyothi S. Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore 560034, Karnataka, India
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Charlton PV, O'Reilly D, Philippou Y, Rao SR, Lamb ADG, Mills IG, Higgins GS, Hamdy FC, Verrill C, Buffa FM, Bryant RJ. Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease. Prostate 2024. [PMID: 38654435 DOI: 10.1002/pros.24715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND It is important to identify molecular features that improve prostate cancer (PCa) risk stratification before radical treatment with curative intent. Molecular analysis of historical diagnostic formalin-fixed paraffin-embedded (FFPE) prostate biopsies from cohorts with post-radiotherapy (RT) long-term clinical follow-up has been limited. Utilizing parallel sequencing modalities, we performed a proof-of-principle sequencing analysis of historical diagnostic FFPE prostate biopsies. We compared patients with (i) stable PCa (sPCa) postprimary or salvage RT, (ii) progressing PCa (pPCa) post-RT, and (iii) de novo metastatic PCa (mPCa). METHODS A cohort of 19 patients with diagnostic prostate biopsies (n = 6 sPCa, n = 5 pPCa, n = 8 mPCa) and mean 4 years 10 months follow-up (diagnosed 2009-2016) underwent nucleic acid extraction from demarcated malignancy. Samples underwent 3'RNA sequencing (3'RNAseq) (n = 19), nanoString analysis (n = 12), and Illumina 850k methylation (n = 8) sequencing. Bioinformatic analysis was performed to coherently identify differentially expressed genes and methylated genomic regions (MGRs). RESULTS Eighteen of 19 samples provided useable 3'RNAseq data. Principal component analysis (PCA) demonstrated similar expression profiles between pPCa and mPCa cases, versus sPCa. Coherently differentially methylated probes between these groups identified ~600 differentially MGRs. The top 50 genes with increased expression in pPCa patients were associated with reduced progression-free survival post-RT (p < 0.0001) in an external cohort. CONCLUSIONS 3'RNAseq, nanoString and 850k-methylation analyses are each achievable from historical FFPE diagnostic pretreatment prostate biopsies, unlocking the potential to utilize large cohorts of historic clinical samples. Profiling similarities between individuals with pPCa and mPCa suggests biological similarities and historical radiological staging limitations, which warrant further investigation.
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Affiliation(s)
- Philip Vincent Charlton
- Department of Oncology, University of Oxford, Oxford, UK
- Department of Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Dawn O'Reilly
- Department of Oncology, University of Oxford, Oxford, UK
| | - Yiannis Philippou
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Srinivasa Rao Rao
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Alastair David Gordon Lamb
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Ian Geoffrey Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Geoff Stuart Higgins
- Department of Oncology, University of Oxford, Oxford, UK
- Department of Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Freddie Charles Hamdy
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Richard John Bryant
- Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
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He X, Hu S, Wang C, Yang Y, Li Z, Zeng M, Song G, Li Y, Lu Q. Predicting prostate cancer recurrence: Introducing PCRPS, an advanced online web server. Heliyon 2024; 10:e28878. [PMID: 38623253 PMCID: PMC11016622 DOI: 10.1016/j.heliyon.2024.e28878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
Background Prostate cancer (PCa) is one of the leading causes of cancer death in men. About 30% of PCa will develop a biochemical recurrence (BCR) following initial treatment, which significantly contributes to prostate cancer-related deaths. In clinical practice, accurate prediction of PCa recurrence is crucial for making informed treatment decisions. However, the development of reliable models and biomarkers for predicting PCa recurrence remains a challenge. In this study, the aim is to establish an effective and reliable tool for predicting the recurrence of PCa. Methods We systematically screened and analyzed potential datasets to predict PCa recurrence. Through quality control analysis, low-quality datasets were removed. Using meta-analysis, differential expression analysis, and feature selection, we identified key genes associated with recurrence. We also evaluated 22 previously published signatures for PCa recurrence prediction. To assess prediction performance, we employed nine machine learning algorithms. We compared the predictive capabilities of models constructed using clinical variables, expression data, and their combinations. Subsequently, we implemented these machine learning models into a user-friendly web server freely accessible to all researchers. Results Based on transcriptomic data derived from eight multicenter studies consisting of 733 PCa patients, we screened 23 highly influential genes for predicting prostate cancer recurrence. These genes were used to construct the Prostate Cancer Recurrence Prediction Signature (PCRPS). By comparing with 22 published signatures and four important clinicopathological features, the PCRPS exhibited a robust and significantly improved predictive capability. Among the tested algorithms, Random Forest demonstrated the highest AUC value of 0.72 in predicting PCa recurrence in the testing dataset. To facilitate access and usage of these machine learning models by all researchers and clinicians, we also developed an online web server (https://urology1926.shinyapps.io/PCRPS/) where the PCRPS model can be freely utilized. The tool can also be used to (1) predict the PCa recurrence by clinical information or expression data with high accuracy. (2) provide the possibility of PCa recurrence by nine machine learning algorithms. Furthermore, using the PCRPS scores, we predicted the sensitivity of 22 drugs from GDSC2 and 95 drugs from CTRP2 to the samples. These predictions provide valuable insights into potential drug sensitivities related to the PCRPS score groups. Conclusion Overall, our study provides an attractive tool to further guide the clinical management and individualized treatment for PCa.
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Affiliation(s)
| | | | - Chen Wang
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Yongjun Yang
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Zhuo Li
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Mingqiang Zeng
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Guangqing Song
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Yuanwei Li
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Qiang Lu
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
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Luo Q, Li X, Meng Z, Rong H, Li Y, Zhao G, Zhu H, Cen L, Liao Q. Identification of hypoxia-related gene signatures based on multi-omics analysis in lung adenocarcinoma. J Cell Mol Med 2024; 28:e18032. [PMID: 38013642 PMCID: PMC10826438 DOI: 10.1111/jcmm.18032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common type of lung cancer and one of the malignancies with the highest incidence rate and mortality worldwide. Hypoxia is a typical feature of tumour microenvironment (TME), which affects the progression of LUAD from multiple molecular levels. However, the underlying molecular mechanisms behind LUAD hypoxia are not fully understood. In this study, we estimated the level of hypoxia by calculating a score based on 15 hypoxia genes. The hypoxia scores were relatively high in LUAD patients with poor prognosis and were bound up with tumour node metastasis (TNM) stage, tumour size, lymph node, age and gender. By comparison of high hypoxia score group and low hypoxia score group, 1820 differentially expressed genes were identified, among which up-regulated genes were mainly about cell division and proliferation while down-regulated genes were primarily involved in cilium-related biological processes. Besides, LUAD patients with high hypoxia scores had higher frequencies of gene mutations, among which TP53, TTN and MUC16 had the highest mutation rates. As for DNA methylation, 1015 differentially methylated probes-related genes were found and may play potential roles in tumour-related neurobiological processes and cell signal transduction. Finally, a prognostic model with 25 multi-omics features was constructed and showed good predictive performance. The area under curve (AUC) values of 1-, 3- and 5-year survival reached 0.863, 0.826 and 0.846, respectively. Above all, our findings are helpful in understanding the impact and molecular mechanisms of hypoxia in LUAD.
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Affiliation(s)
- Qineng Luo
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Xing Li
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Zixing Meng
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Hao Rong
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Yanguo Li
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
| | - Guofang Zhao
- Department of Thoracic SurgeryHwa Mei HospitalUniversity of Chinese Academy of SciencesNingboZhejiangP. R. China
| | - Huangkai Zhu
- Department of Thoracic SurgeryHwa Mei HospitalUniversity of Chinese Academy of SciencesNingboZhejiangP. R. China
| | - Lvjun Cen
- The First Affiliated HospitalNingbo UniversityNingboZhejiangP. R. China
| | - Qi Liao
- School of Public HealthHealth Science CenterNingbo UniversityNingboZhejiangP. R. China
- The First Affiliated HospitalNingbo UniversityNingboZhejiangP. R. China
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An Y, Lu W, Li S, Lu X, Zhang Y, Han D, Su D, Jia J, Yuan J, Zhao B, Tu M, Li X, Wang X, Fang N, Ji S. Systematic review and integrated analysis of prognostic gene signatures for prostate cancer patients. Discov Oncol 2023; 14:234. [PMID: 38112859 PMCID: PMC10730790 DOI: 10.1007/s12672-023-00847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
Prostate cancer (PC) is one of the most common cancers in men and becoming the second leading cause of cancer fatalities. At present, the lack of effective strategies for prognosis of PC patients is still a problem to be solved. Therefore, it is significant to identify potential gene signatures for PC patients' prognosis. Here, we summarized 71 different prognostic gene signatures for PC and concluded 3 strategies for signature construction after extensive investigation. In addition, 14 genes frequently appeared in 71 different gene signatures, which enriched in mitotic and cell cycle. This review provides extensive understanding and integrated analysis of current prognostic signatures of PC, which may help researchers to construct gene signatures of PC and guide future clinical treatment.
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Affiliation(s)
- Yang An
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China.
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China.
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China.
| | - Wenyuan Lu
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Shijia Li
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Xiaoyan Lu
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Yuanyuan Zhang
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Dongcheng Han
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Dingyuan Su
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Jiaxin Jia
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Jiaxin Yuan
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Binbin Zhao
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Mengjie Tu
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Xinyu Li
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Xiaoqing Wang
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China
| | - Na Fang
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China.
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China.
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China.
| | - Shaoping Ji
- School of Basic Medical Sciences, Henan University, Kaifeng, 475004, China.
- Department of Biochemistry and Molecular Biology, Cell Signal Transduction Laboratory, School of Basic Medical Sciences, Henan University, Jinming Street, Kaifeng, 475004, Henan, China.
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Kaifeng, 475004, China.
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Abou Khouzam R, Janji B, Thiery J, Zaarour RF, Chamseddine AN, Mayr H, Savagner P, Kieda C, Gad S, Buart S, Lehn JM, Limani P, Chouaib S. Hypoxia as a potential inducer of immune tolerance, tumor plasticity and a driver of tumor mutational burden: Impact on cancer immunotherapy. Semin Cancer Biol 2023; 97:104-123. [PMID: 38029865 DOI: 10.1016/j.semcancer.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
In cancer patients, immune cells are often functionally compromised due to the immunosuppressive features of the tumor microenvironment (TME) which contribute to the failures in cancer therapies. Clinical and experimental evidence indicates that developing tumors adapt to the immunological environment and create a local microenvironment that impairs immune function by inducing immune tolerance and invasion. In this context, microenvironmental hypoxia, which is an established hallmark of solid tumors, significantly contributes to tumor aggressiveness and therapy resistance through the induction of tumor plasticity/heterogeneity and, more importantly, through the differentiation and expansion of immune-suppressive stromal cells. We and others have provided evidence indicating that hypoxia also drives genomic instability in cancer cells and interferes with DNA damage response and repair suggesting that hypoxia could be a potential driver of tumor mutational burden. Here, we reviewed the current knowledge on how hypoxic stress in the TME impacts tumor angiogenesis, heterogeneity, plasticity, and immune resistance, with a special interest in tumor immunogenicity and hypoxia targeting. An integrated understanding of the complexity of the effect of hypoxia on the immune and microenvironmental components could lead to the identification of better adapted and more effective combinational strategies in cancer immunotherapy. Clearly, the discovery and validation of therapeutic targets derived from the hypoxic tumor microenvironment is of major importance and the identification of critical hypoxia-associated pathways could generate targets that are undeniably attractive for combined cancer immunotherapy approaches.
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Affiliation(s)
- Raefa Abou Khouzam
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates.
| | - Bassam Janji
- Department of Cancer Research, Luxembourg Institute of Health, Tumor Immunotherapy and Microenvironment (TIME) Group, 6A, rue Nicolas-Ernest Barblé, L-1210 Luxembourg city, Luxembourg.
| | - Jerome Thiery
- INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculty of Medicine, University Paris-Saclay, 94805 Villejuif, France.
| | - Rania Faouzi Zaarour
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates.
| | - Ali N Chamseddine
- Gastroenterology Department, Cochin University Hospital, Université de Paris, APHP, Paris, France; Ambroise Paré - Hartmann Private Hospital Group, Oncology Unit, Neuilly-sur-Seine, France.
| | - Hemma Mayr
- Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, University Hospital Zurich, Raemistrasse 100, Zurich, Switzerland; Department of Surgery & Transplantation, University and University Hospital Zurich, Raemistrasse 100, Zurich, Switzerland.
| | - Pierre Savagner
- INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculty of Medicine, University Paris-Saclay, 94805 Villejuif, France.
| | - Claudine Kieda
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine-National Research Institute, 04-141 Warsaw, Poland; Centre for Molecular Biophysics, UPR 4301 CNRS, 45071 Orleans, France; Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland.
| | - Sophie Gad
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences Lettres University (PSL), 75014 Paris, France; UMR CNRS 9019, Genome Integrity and Cancers, Gustave Roussy, Paris-Saclay University, 94800 Villejuif, France.
| | - Stéphanie Buart
- INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculty of Medicine, University Paris-Saclay, 94805 Villejuif, France.
| | - Jean-Marie Lehn
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, Strasbourg, France.
| | - Perparim Limani
- Swiss Hepato-Pancreato-Biliary (HPB) and Transplantation Center, University Hospital Zurich, Raemistrasse 100, Zurich, Switzerland; Department of Surgery & Transplantation, University and University Hospital Zurich, Raemistrasse 100, Zurich, Switzerland.
| | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates; INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculty of Medicine, University Paris-Saclay, 94805 Villejuif, France.
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7
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Cohn DE, Forder A, Marshall EA, Vucic EA, Stewart GL, Noureddine K, Lockwood WW, MacAulay CE, Guillaud M, Lam WL. Delineating spatial cell-cell interactions in the solid tumour microenvironment through the lens of highly multiplexed imaging. Front Immunol 2023; 14:1275890. [PMID: 37936700 PMCID: PMC10627006 DOI: 10.3389/fimmu.2023.1275890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023] Open
Abstract
The growth and metastasis of solid tumours is known to be facilitated by the tumour microenvironment (TME), which is composed of a highly diverse collection of cell types that interact and communicate with one another extensively. Many of these interactions involve the immune cell population within the TME, referred to as the tumour immune microenvironment (TIME). These non-cell autonomous interactions exert substantial influence over cell behaviour and contribute to the reprogramming of immune and stromal cells into numerous pro-tumourigenic phenotypes. The study of some of these interactions, such as the PD-1/PD-L1 axis that induces CD8+ T cell exhaustion, has led to the development of breakthrough therapeutic advances. Yet many common analyses of the TME either do not retain the spatial data necessary to assess cell-cell interactions, or interrogate few (<10) markers, limiting the capacity for cell phenotyping. Recently developed digital pathology technologies, together with sophisticated bioimage analysis programs, now enable the high-resolution, highly-multiplexed analysis of diverse immune and stromal cell markers within the TME of clinical specimens. In this article, we review the tumour-promoting non-cell autonomous interactions in the TME and their impact on tumour behaviour. We additionally survey commonly used image analysis programs and highly-multiplexed spatial imaging technologies, and we discuss their relative advantages and limitations. The spatial organization of the TME varies enormously between patients, and so leveraging these technologies in future studies to further characterize how non-cell autonomous interactions impact tumour behaviour may inform the personalization of cancer treatment..
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Affiliation(s)
- David E. Cohn
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Aisling Forder
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Erin A. Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Emily A. Vucic
- Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Langone Medical Center, New York, NY, United States
| | - Greg L. Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Kouther Noureddine
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - William W. Lockwood
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Calum E. MacAulay
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Martial Guillaud
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Wan L. Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
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8
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Gui C, Wei J, Mo C, Liang Y, Cen J, Chen Y, Wang D, Luo J. Therapeutic implications for localized prostate cancer by multiomics analyses of the ageing microenvironment landscape. Int J Biol Sci 2023; 19:3951-3969. [PMID: 37564213 PMCID: PMC10411471 DOI: 10.7150/ijbs.85209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
Background: Numerous studies have substantiated the association between aging and the progression of malignant tumors in humans, notably prostate cancer (PCa). Nevertheless, to the best of our knowledge, no studies have comprehensively elucidated the intricate characteristics of the aging microenvironment (AME) in PCa. Methods: AME regulatory patterns were determined using the NMF algorithm. Then an ageing microenvironment index (AMI) was constructed, with excellent prognostic and immunotherapy prediction ability, and its' clinical relevance was surveyed through spatial transcriptomics. Further, the drug response was analysed using the Genomics of Drug Sensitivity in Cancer (GDSC), the Connectivity Map (CMap) and CellMiner database for patients with PCa. Finally, the AME was studied using in vitro and vivo experiments. Results: Three different AME regulatory patterns were identified across 813 PCa patients, associated with distinct clinical prognosis and physiological pathways. Based on the AMI, patients with PCa were divided into the high-score and low-score subsets. Higher AMI score was significantly infiltrated with more immune cells, higher rate of biochemical recurrence (BCR) and worse response to immunotherapy, antiandrogen therapy and chemotherapy in PCa. In addition, we found that the combination of bicalutamide and embelin was capable of suppressing tumor growth of PCa. Besides, as the main components of AMI, COL1A1 and BGLAP act as oncogenes and were verified via in vivo and in vitro experiments. Conclusions: AME regulation is significantly associated with the diversity and complexity of TME. Quantitative evaluation of the AME regulatory patterns may provide promising novel molecular markers for individualised therapy in PCa.
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Affiliation(s)
- Chengpeng Gui
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jinhuan Wei
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chengqiang Mo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yanping Liang
- Department of Laboratory Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junjie Cen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuhang Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Daohu Wang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junhang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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9
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Zhong J, Frood R, McWilliam A, Davey A, Shortall J, Swinton M, Hulson O, West CM, Buckley D, Brown S, Choudhury A, Hoskin P, Henry A, Scarsbrook A. Prediction of prostate tumour hypoxia using pre-treatment MRI-derived radiomics: preliminary findings. LA RADIOLOGIA MEDICA 2023; 128:765-774. [PMID: 37198374 PMCID: PMC10264289 DOI: 10.1007/s11547-023-01644-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023]
Abstract
PURPOSE To develop a machine learning (ML) model based on radiomic features (RF) extracted from whole prostate gland magnetic resonance imaging (MRI) for prediction of tumour hypoxia pre-radiotherapy. MATERIAL AND METHODS Consecutive patients with high-grade prostate cancer and pre-treatment MRI treated with radiotherapy between 01/12/2007 and 1/08/2013 at two cancer centres were included. Cancers were dichotomised as normoxic or hypoxic using a biopsy-based 32-gene hypoxia signature (Ragnum signature). Prostate segmentation was performed on axial T2-weighted (T2w) sequences using RayStation (v9.1). Histogram standardisation was applied prior to RF extraction. PyRadiomics (v3.0.1) was used to extract RFs for analysis. The cohort was split 80:20 into training and test sets. Six different ML classifiers for distinguishing hypoxia were trained and tuned using five different feature selection models and fivefold cross-validation with 20 repeats. The model with the highest mean validation area under the curve (AUC) receiver operating characteristic (ROC) curve was tested on the unseen set, and AUCs were compared via DeLong test with 95% confidence interval (CI). RESULTS 195 patients were included with 97 (49.7%) having hypoxic tumours. The hypoxia prediction model with best performance was derived using ridge regression and had a test AUC of 0.69 (95% CI: 0.14). The test AUC for the clinical-only model was lower (0.57), but this was not statistically significant (p = 0.35). The five selected RFs included textural and wavelet-transformed features. CONCLUSION Whole prostate MRI-radiomics has the potential to non-invasively predict tumour hypoxia prior to radiotherapy which may be helpful for individualised treatment optimisation.
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Affiliation(s)
- Jim Zhong
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
- Department of Radiology, Leeds Cancer Centre, St James's University Hospital, Leeds Teaching Hospitals National Health Service (NHS) Trust, Beckett Street, Leeds, LS9 7TF, UK.
| | - Russell Frood
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Radiology, Leeds Cancer Centre, St James's University Hospital, Leeds Teaching Hospitals National Health Service (NHS) Trust, Beckett Street, Leeds, LS9 7TF, UK
| | - Alan McWilliam
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, UK
| | - Angela Davey
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, UK
| | - Jane Shortall
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, UK
| | - Martin Swinton
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, UK
| | - Oliver Hulson
- Department of Radiology, Leeds Cancer Centre, St James's University Hospital, Leeds Teaching Hospitals National Health Service (NHS) Trust, Beckett Street, Leeds, LS9 7TF, UK
| | - Catharine M West
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - David Buckley
- Biomedical Imaging, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Sarah Brown
- Leeds Cancer Research UK Clinical Trials Unit, Leeds Institute of Clinical Trials Research (LICTR), University of Leeds, Leeds, UK
| | - Ananya Choudhury
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, UK
| | - Peter Hoskin
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Department of Radiotherapy Related Research, The Christie National Health Service (NHS) Foundation Trust, Manchester, UK
| | - Ann Henry
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Clinical Oncology, Leeds Cancer Centre, St James's University Hospital, Leeds Teaching Hospitals National Health Service (NHS) Trust, Beckett Street, Leeds, LS9 7TF, UK
| | - Andrew Scarsbrook
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Radiology, Leeds Cancer Centre, St James's University Hospital, Leeds Teaching Hospitals National Health Service (NHS) Trust, Beckett Street, Leeds, LS9 7TF, UK
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10
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Ogbonnaya CN, Alsaedi BSO, Alhussaini AJ, Hislop R, Pratt N, Nabi G. Radiogenomics Reveals Correlation between Quantitative Texture Radiomic Features of Biparametric MRI and Hypoxia-Related Gene Expression in Men with Localised Prostate Cancer. J Clin Med 2023; 12:jcm12072605. [PMID: 37048688 PMCID: PMC10095552 DOI: 10.3390/jcm12072605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVES To perform multiscale correlation analysis between quantitative texture feature phenotypes of pre-biopsy biparametric MRI (bpMRI) and targeted sequence-based RNA expression for hypoxia-related genes. MATERIALS AND METHODS Images from pre-biopsy 3T bpMRI scans in clinically localised PCa patients of various risk categories (n = 15) were used to extract textural features. The genomic landscape of hypoxia-related gene expression was obtained using post-radical prostatectomy tissue for targeted RNA expression profiling using the TempO-sequence method. The nonparametric Games Howell test was used to correlate the differential expression of the important hypoxia-related genes with 28 radiomic texture features. Then, cBioportal was accessed, and a gene-specific query was executed to extract the Oncoprint genomic output graph of the selected hypoxia-related genes from The Cancer Genome Atlas (TCGA). Based on each selected gene profile, correlation analysis using Pearson's coefficients and survival analysis using Kaplan-Meier estimators were performed. RESULTS The quantitative bpMR imaging textural features, including the histogram and grey level co-occurrence matrix (GLCM), correlated with three hypoxia-related genes (ANGPTL4, VEGFA, and P4HA1) based on RNA sequencing using the TempO-Seq method. Further radiogenomic analysis, including data accessed from the cBioportal genomic database, confirmed that overexpressed hypoxia-related genes significantly correlated with a poor survival outcomes, with a median survival ratio of 81.11:133.00 months in those with and without alterations in genes, respectively. CONCLUSION This study found that there is a correlation between the radiomic texture features extracted from bpMRI in localised prostate cancer and the hypoxia-related genes that are differentially expressed. The analysis of expression data based on cBioportal revealed that these hypoxia-related genes, which were the focus of the study, are linked to an unfavourable survival outcomes in prostate cancer patients.
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Affiliation(s)
- Chidozie N Ogbonnaya
- Division of Imaging Science and Technology, University of Dundee, Dundee DD1 4HN, UK
- College of Basic Medical Sciences, Abia State University, Uturu 441103, Nigeria
| | - Basim S O Alsaedi
- Statistics Department, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Abeer J Alhussaini
- Division of Imaging Science and Technology, University of Dundee, Dundee DD1 4HN, UK
- Department of Medical Imaging, Al-Amiri Hospital, Ministry of Health, Sulaibikhat 1300, Kuwait
| | - Robert Hislop
- Cytogenetic, Human Genetics Unit, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Norman Pratt
- Cytogenetic, Human Genetics Unit, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Ghulam Nabi
- Division of Imaging Science and Technology, University of Dundee, Dundee DD1 4HN, UK
- School of Medicine, Ninewells Hospital, Dundee DD1 9SY, UK
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11
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Ma C, Zhou Y, Fanelli GN, Stopsack KH, Fiorentino M, Zadra G, Mucci LA, Loda M, Tyekucheva S, Penney KL. The Prostate Stromal Transcriptome in Aggressive and Lethal Prostate Cancer. Mol Cancer Res 2023; 21:253-260. [PMID: 36511902 PMCID: PMC9991973 DOI: 10.1158/1541-7786.mcr-22-0627] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/01/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Prostate cancer has a heterogeneous prognosis. Most previous studies have focused on the identification of prognostic biomarkers in the prostate cancer tumor. However, it is increasingly recognized that the tumor microenvironment contributes to prostate cancer aggressiveness and progression. We therefore examined whole transcriptome expression of the prostate stroma and associations with aggressive and lethal prostate cancer. We performed RNA sequencing (Illumina TruSeq Exome Capture) of 272 tumor-adjacent and 120 benign-adjacent macrodissected prostate stromal samples from 293 men with prostate cancer from the Health Professionals Follow-up Study and Physicians' Health Study. We performed differential expression analysis comparing gene expression and pathways by Gleason score and lethal outcome. We also tested a previously developed stromal gene signature of Gleason score in these datasets. Comparing high- with low-Gleason score cancers, 26 genes (P < 0.001) and 12 pathways (FDR < 0.20) were significantly differentially expressed in tumor-adjacent stroma, including pathways related to stroma composition remodeling and DNA repair, with 73 genes and 65 pathways significant in benign-adjacent stroma. Comparing lethal with nonlethal prostate cancer, 11 genes were differentially expressed in tumor-adjacent and 15 genes in benign-adjacent stroma, and pathways involved in inflammatory response were differentially enriched in both tumor and benign-adjacent stroma. In addition, our previously identified Gleason stromal gene signature was validated to be associated with Gleason score in these data. Implications: Our study uncovers stroma-specific genes and pathways that are differentially enriched with high Gleason score and lethal prostate cancer, demonstrating that the molecular investigation of the tumor microenvironment can provide additional information about prostate cancer prognosis.
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Affiliation(s)
- Chaoran Ma
- Brigham and Women’s Hospital/Harvard Medical School, Boston, MA
| | | | | | | | | | - Giorgia Zadra
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | | | | | - Svitlana Tyekucheva
- Dana-Farber Cancer Institute, Boston, MA
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - Kathryn L. Penney
- Brigham and Women’s Hospital/Harvard Medical School, Boston, MA
- Harvard T.H. Chan School of Public Health, Boston, MA
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12
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Angel CZ, Stafford MYC, McNally CJ, Nesbitt H, McKenna DJ. MiR-21 Is Induced by Hypoxia and Down-Regulates RHOB in Prostate Cancer. Cancers (Basel) 2023; 15:cancers15041291. [PMID: 36831632 PMCID: PMC9954526 DOI: 10.3390/cancers15041291] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Tumour hypoxia is a well-established contributor to prostate cancer progression and is also known to alter the expression of several microRNAs. The over-expression of microRNA-21 (miR-21) has been consistently linked with many cancers, but its role in the hypoxic prostate tumour environment has not been well studied. In this paper, the link between hypoxia and miR-21 in prostate cancer is investigated. A bioinformatic analysis of The Cancer Genome Atlas (TCGA) prostate biopsy datasets shows the up-regulation of miR-21 is significantly associated with prostate cancer and clinical markers of disease progression. This up-regulation of miR-21 expression was shown to be caused by hypoxia in the LNCaP prostate cancer cell line in vitro and in an in vivo prostate tumour xenograft model. A functional enrichment analysis also revealed a significant association of miR-21 and its target genes with processes related to cellular hypoxia. The over-expression of miR-21 increased the migration and colony-forming ability of RWPE-1 normal prostate cells. In vitro and in silico analyses demonstrated that miR-21 down-regulates the tumour suppressor gene Ras Homolog Family Member B (RHOB) in prostate cancer. Further a TCGA analysis illustrated that miR-21 can distinguish between different patient outcomes following therapy. This study presents evidence that hypoxia is a key contributor to the over-expression of miR-21 in prostate tumours, which can subsequently promote prostate cancer progression by suppressing RHOB expression. We propose that miR-21 has good potential as a clinically useful diagnostic and prognostic biomarker of hypoxia and prostate cancer.
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Affiliation(s)
- Charlotte Zoe Angel
- Genomic Medicine Research Group, Ulster University, Cromore Road, Coleraine BT52 1SA, UK
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | | | - Christopher J. McNally
- Genomic Medicine Research Group, Ulster University, Cromore Road, Coleraine BT52 1SA, UK
| | - Heather Nesbitt
- Genomic Medicine Research Group, Ulster University, Cromore Road, Coleraine BT52 1SA, UK
| | - Declan J. McKenna
- Genomic Medicine Research Group, Ulster University, Cromore Road, Coleraine BT52 1SA, UK
- Correspondence:
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13
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Sun H, Li Y, Zhang Y, Zhao X, Dong X, Guo Y, Mo J, Che N, Ban X, Li F, Bai X, Li Y, Hao J, Zhang D. The relevance between hypoxia-dependent spatial transcriptomics and the prognosis and efficacy of immunotherapy in claudin-low breast cancer. Front Immunol 2023; 13:1042835. [PMID: 36685583 PMCID: PMC9846556 DOI: 10.3389/fimmu.2022.1042835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Hypoxia is an important characteristic of solid tumors. However, spatial transcriptomics (ST) of hypoxia-associated heterogeneity is not clear. Methods This study integrated Spatial Transcriptomics (ST) with immunofluorescence to demonstrate their spatial distribution in human claudin-low breast cancer MDA-MB-231 engraft. ST spots were clustered with differentially expression genes. The data were combined with hypoxia-specific marker and angiogenesis marker-labeled serial sections to indicate the spatial distribution of hypoxia and hypoxia-inducted transcriptional profile. Moreover, marker genes, cluster-specific hypoxia genes, and their co-essential relationship were identified and mapped in every clusters. The clinicopathological association of marker genes of hypoxia-dependent spatial clusters was explored in 1904 breast cancers from METABRIC database. Results The tumor from center to periphery were enriched into five hypoxia-dependent subgroups with differentially expressed genes, which were matched to necrosis, necrosis periphery, hypoxic tumor, adaptive survival tumor, and invasive tumor, respectively. Different subgroups demonstrated distinct hypoxia condition and spatial heterogeneity in biological behavior and signaling pathways. Cox regression analysis showed that the invasive tumor (cluster 0) and hypoxic tumor (cluster 6) score could be served as independent prognostic factors in claudin-low patients. KM analysis indicated that high invasive tumor (cluster 0) and hypoxic tumor (cluster 6) score was associated with poor prognoses of claudin-low patients. Further analysis showed that hypoxia-induced immune checkpoints, such as CD276 and NRP1, upregulation in invasive tumor to block infiltration and activation of B cells and CD8+ T cells to change tumor immune microenvironment. Discussion This study reveals hypoxia-dependent spatial heterogeneity in claudin-low breast cancer and highlights its potential value as a predictive biomarker of clinical outcomes and immunotherapy response. The molecules found in this study also provided potential molecular mechanisms and therapeutic targets for subsequent studies.
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Affiliation(s)
- Huizhi Sun
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Yanlei Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Yanhui Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Xiulan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xueyi Dong
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Yuhong Guo
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Jing Mo
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Na Che
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xinchao Ban
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Fan Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xiaoyu Bai
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Yue Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Jihui Hao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Danfang Zhang
- Department of Pathology, Tianjin Medical University, Tianjin, China
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14
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Yang C, Chen L, Niu Q, Ge Q, Zhang J, Tao J, Zhou J, Liang C. Identification and validation of an E2F-related gene signature for predicting recurrence-free survival in human prostate cancer. Cancer Cell Int 2022; 22:382. [PMID: 36471446 PMCID: PMC9721026 DOI: 10.1186/s12935-022-02791-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND It is well-established that biochemical recurrence is detrimental to prostate cancer (PCa). In the present study, we explored the mechanisms underlying PCa progression. METHODS Five cohorts from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases were used to perform gene set variation analysis (GSVA) between nonrecurrent and recurrent PCa patients. We obtained the intersection of pathway enrichment results and extracted the corresponding gene list. LASSO Cox regression analysis was used to identify recurrence-free survival (RFS)-related significant genes and establish an RFS prediction gene signature and nomogram. MTT and colony formation assays were conducted to validate our findings. RESULTS The E2F signaling pathway was activated in recurrent PCa patients compared to nonrecurrent patients. We established an E2F-related gene signature for RFS prediction based on the four identified E2F-related genes (CDKN2C, CDKN3, RACGAP1, and RRM2) using LASSO Cox regression in the Memorial Sloan Kettering Cancer Center (MSKCC) cohort. The risk score of each patient in MSKCC was calculated based on the expression levels of CDKN2C, CDKN3, RACGAP1, and RRM2. PCa patients with low-risk scores exhibited higher RFS than those with high-risk scores. Receiver operating characteristic (ROC) curve analysis validated the good performance and prognostic accuracy of the E2F-related gene signature, which was validated in the TCGA-prostate adenocarcinoma (TCGA-PRAD) cohort. Compared to patients with low Gleason scores and early T stages, PCa patients with high Gleason scores and advanced T stages had high-risk scores. Moreover, the E2F-related gene signature-based nomogram yielded good performance in RFS prediction. Functional experiments further confirmed these results. CONCLUSIONS The E2F signaling pathway is associated with biochemical recurrence in PCa. Our established E2F-related gene signature and nomogram yielded good accuracy in predicting the biochemical recurrence in PCa.
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Affiliation(s)
- Cheng Yang
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
| | - Lei Chen
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
| | - Qingsong Niu
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
| | - Qintao Ge
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
| | - Jiong Zhang
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
| | - Junyue Tao
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
| | - Jun Zhou
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
| | - Chaozhao Liang
- grid.412679.f0000 0004 1771 3402Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XInstitute of Urology, Anhui Medical University, Hefei, China ,grid.186775.a0000 0000 9490 772XAnhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Jixi Road 218, Shushan District, Hefei City, 230022 Anhui Province People’s Republic of China
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15
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Yimamu Y, Yang X, Chen J, Luo C, Xiao W, Guan H, Wang D. The Development of a Gleason Score-Related Gene Signature for Predicting the Prognosis of Prostate Cancer. J Clin Med 2022; 11:jcm11237164. [PMID: 36498737 PMCID: PMC9737657 DOI: 10.3390/jcm11237164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
The recurrence of prostate cancer (PCa) is intrinsically linked to increased mortality. The goal of this study was to develop an efficient and reliable prognosis prediction signature for PCa patients. The training cohort was acquired from The Cancer Genome Atlas (TCGA) dataset, while the validation cohort was obtained from the Gene Expression Omnibus (GEO) dataset (GSE70769). To explore the Gleason score (GS)-based prediction signature, we screened the differentially expressed genes (DEGs) between low- and high-GS groups, and then univariate Cox regression survival analysis and multiple Cox analyses were performed sequentially using the training cohort. The testing cohort was used to evaluate and validate the prognostic model's effectiveness, accuracy, and clinical practicability. In addition, the correlation analyses between the risk score and clinical features, as well as immune infiltration, were performed. We constructed and optimized a valid and credible model for predicting the prognosis of PCa recurrence using four GS-associated genes (SFRP4, FEV, COL1A1, SULF1). Furthermore, ROC and Kaplan-Meier analysis revealed a higher predictive efficiency for biochemical recurrence (BCR). The results showed that the risk model was an independent prognostic factor. Moreover, the risk score was associated with clinical features and immune infiltration. Finally, the risk model was validated in a testing cohort. Our data support that the GS-based four-gene signature acts as a novel signature for predicting BCR in PCa patients.
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Affiliation(s)
- Yiliyasi Yimamu
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Xu Yang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Junxin Chen
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Cheng Luo
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Wenyang Xiao
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Hongyu Guan
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Daohu Wang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
- Correspondence:
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16
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Lombardi O, Li R, Halim S, Choudhry H, Ratcliffe PJ, Mole DR. Pan-cancer analysis of tissue and single-cell HIF-pathway activation using a conserved gene signature. Cell Rep 2022; 41:111652. [PMID: 36384128 PMCID: PMC9869179 DOI: 10.1016/j.celrep.2022.111652] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/05/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
Activation of cellular hypoxia pathways, orchestrated by HIF (hypoxia-inducible factor) transcription factors, is a common feature of multiple tumor types, resulting from microenvironment factors and oncogenic mutation. Although they help drive many of the "hallmarks" of cancer and are associated with poor outcome and resistance to therapy, the transcriptional targets of HIF vary considerably depending on the cell type. By integrating 72 genome-wide assays of HIF binding and transcriptional regulation from multiple cancer types, we define a consensus set of 48 HIF target genes that is highly conserved across cancer types and cell lineages. These genes provide an effective marker of HIF activation in bulk and single-cell transcriptomic analyses across a wide range of cancer types and in malignant and stromal cell types. This allows the tissue-orchestrated responses to the hypoxic tumor microenvironment and to oncogenic HIF activation to be deconvoluted at the tumor and single-cell level.
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Affiliation(s)
- Olivia Lombardi
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Ran Li
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Silvia Halim
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Peter J Ratcliffe
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David R Mole
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK.
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A systematic study of HIF1A cofactors in hypoxic cancer cells. Sci Rep 2022; 12:18962. [PMID: 36347941 PMCID: PMC9643333 DOI: 10.1038/s41598-022-23060-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Hypoxia inducible factor 1 alpha (HIF1A) is a transcription factor (TF) that forms highly structural and functional protein-protein interactions with other TFs to promote gene expression in hypoxic cancer cells. However, despite the importance of these TF-TF interactions, we still lack a comprehensive view of many of the TF cofactors involved and how they cooperate. In this study, we systematically studied HIF1A cofactors in eight cancer cell lines using the computational motif mining tool, SIOMICS, and discovered 201 potential HIF1A cofactors, which included 21 of the 29 known HIF1A cofactors in public databases. These 201 cofactors were statistically and biologically significant, with 19 of the top 37 cofactors in our study directly validated in the literature. The remaining 18 were novel cofactors. These discovered cofactors can be essential to HIF1A's regulatory functions and may lead to the discovery of new therapeutic targets in cancer treatment.
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18
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Development of an Independent Prognostic Signature Based on Three Hypoxia-Related Genes for Breast Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2974126. [DOI: 10.1155/2022/2974126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Background. Hypoxia was considered to be a prognostic indicator in a variety of solid tumors. This study aims at identifying the hypoxia-related genes (HRGs) in breast cancer (BC) and the feasibility of HRGs as a prognostic indicator. Methods. We downloaded the mRNA expression data of BC patients from TCGA and GEO databases. The LASSO Cox regression analysis was applied to screen the hub HRGs to establish a prognostic Risk Score. The independence of Risk Score was assessed by multivariate Cox regression analysis. And the immune checkpoint analysis was also performed. In addition, we also detected the expression level of hub HRGs in MCF-10A cells, MCF-7 cells, and SK-BR-3 cells by RT-qPCR. Results. Three HRGs were identified as hub genes with prognostic value in BC, including CA9, PGK1, and SDC1. The Risk Score constructed by these three genes could efficiently distinguish the prognosis of different BC patients and has been shown to be an independent prognostic indicator. In the high-risk group, patients had lower overall survival and poorer prognosis. In addition, the expression levels of five immune checkpoints (PD1, CTLA4, TIGIT, LAG3, and TIM3) in the high-risk group were significantly higher than those in the low-risk group. Moreover, the expression levels of PGK1 and SDC1 in BC cells were significantly increased. Conclusion. In this study, we established an efficiently model based on three optimal HRGs (CA9, PGK1, and SDC1) could clearly distinguish the prognosis of different BC patients.
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Zhang R, Liu F. Cancer-associated fibroblast-derived gene signatures predict radiotherapeutic survival in prostate cancer patients. J Transl Med 2022; 20:453. [PMID: 36195908 PMCID: PMC9533530 DOI: 10.1186/s12967-022-03656-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/20/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) play multiple roles in regulating tumor metastasis and treatment response. Current clinical indicators are insufficient to accurately assess disease risk and radiotherapy response, emphasizing the urgent need for additional molecular prognostic markers. METHODS In order to investigate CAF-related genes associated with radiotherapy and construct prognostic CAF-related gene signatures for prostate cancer, we firstly established a radio-resistant prostate CAF cell subline (referred to as CAFR) from Mus-CAF (referred to as CAF) through fractionated irradiation using X-rays. Transcriptome sequencing for CAF and CAFR was conducted, and 2626 CAF-related differentially expressed genes (DEGs) associated with radiotherapy were identified. Human homologous genes of mouse CAF-related DEGs were then obtained. RESULTS Functional enrichment analysis revealed that these CAF-related DEGs were significantly enriched ECM- and immune-related functions and pathways. Based on GSE116918 dataset, 186 CAF-related DEGs were correlated with biochemical recurrence-free survival (BCRFS) of prostate cancer patients, 16 of which were selected to construct a BCRFS-related CAF signature, such as ACPP, THBS2, and KCTD14; 142 CAF-related DEGs were correlated with metastasis-free survival (MFS), 16 of which were used to construct a MFS-related CAF signature, such as HOPX, TMEM132A, and ZNF467. Both Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets confirmed that the two CAF signatures accurately predicted BCRFS and MFS of prostate cancer patients. The risk scores were higher in patients with higher gleason grades and higher clinical T stages. Moreover, the BCRFS-related CAF signature was an independent prognostic factor and a nomogram consisting of BCRFS-related CAF signature and various clinical factors accurately predicted 2-, 3-, and 5-year survival time of prostate cancer patients. Furthermore, the risk score was positively correlated with multiple immune checkpoints. CONCLUSIONS Our established CAF signatures could accurately predict BCRFS and MFS in prostate cancer patients undergoing radiotherapy.
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Affiliation(s)
- Ran Zhang
- Laboratory of Radio-Immunology, Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, People's Republic of China
| | - Feng Liu
- Department of Immunology, School of Biomedical Sciences, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
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20
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d’Hose D, Mathieu B, Mignion L, Hardy M, Ouari O, Jordan BF, Sonveaux P, Gallez B. EPR Investigations to Study the Impact of Mito-Metformin on the Mitochondrial Function of Prostate Cancer Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27185872. [PMID: 36144606 PMCID: PMC9504708 DOI: 10.3390/molecules27185872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022]
Abstract
Background: Mito-metformin10 (MM10), synthesized by attaching a triphenylphosphonium cationic moiety via a 10-carbon aliphatic side chain to metformin, is a mitochondria-targeted analog of metformin that was recently demonstrated to alter mitochondrial function and proliferation in pancreatic ductal adenocarcinoma. Here, we hypothesized that this compound may decrease the oxygen consumption rate (OCR) in prostate cancer cells, increase the level of mitochondrial ROS, alleviate tumor hypoxia, and radiosensitize tumors. Methods: OCR and mitochondrial superoxide production were assessed by EPR (9 GHz) in vitro in PC-3 and DU-145 prostate cancer cells. Reduced and oxidized glutathione were assessed before and after MM10 exposure. Tumor oxygenation was measured in vivo using 1 GHz EPR oximetry in PC-3 tumor model. Tumors were irradiated at the time of maximal reoxygenation. Results: 24-hours exposure to MM10 significantly decreased the OCR of PC-3 and DU-145 cancer cells. An increase in mitochondrial superoxide levels was observed in PC-3 but not in DU-145 cancer cells, an observation consistent with the differences observed in glutathione levels in both cancer cell lines. In vivo, the tumor oxygenation significantly increased in the PC-3 model (daily injection of 2 mg/kg MM10) 48 and 72 h after initiation of the treatment. Despite the significant effect on tumor hypoxia, MM10 combined to irradiation did not increase the tumor growth delay compared to the irradiation alone. Conclusions: MM10 altered the OCR in prostate cancer cells. The effect of MM10 on the superoxide level was dependent on the antioxidant capacity of cell line. In vivo, MM10 alleviated tumor hypoxia, yet without consequence in terms of response to irradiation.
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Affiliation(s)
- Donatienne d’Hose
- Biomedical Magnetic Resonance, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Barbara Mathieu
- Biomedical Magnetic Resonance, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Lionel Mignion
- Biomedical Magnetic Resonance, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Micael Hardy
- Institut de Chimie Radicalaire UMR 7273, Aix-Marseille Université/CNRS, 13013 Marseille, France
| | - Olivier Ouari
- Institut de Chimie Radicalaire UMR 7273, Aix-Marseille Université/CNRS, 13013 Marseille, France
| | - Bénédicte F. Jordan
- Biomedical Magnetic Resonance, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
| | - Pierre Sonveaux
- Pole of Pharmacology and Therapeutics, Institut de Recherches Expérimentales et Cliniques (IREC), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO) Research Institute, 1300 Wavre, Belgium
| | - Bernard Gallez
- Biomedical Magnetic Resonance, Louvain Drug Research Institute (LDRI), Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium
- Correspondence:
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21
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Li J, Guan Y, Zhu R, Wang Y, Zhu H, Wang X. Identification of metabolic genes for the prediction of prognosis and tumor microenvironment infiltration in early-stage non-small cell lung cancer. Open Life Sci 2022; 17:881-892. [PMID: 36045718 PMCID: PMC9372707 DOI: 10.1515/biol-2022-0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/03/2022] [Accepted: 05/03/2022] [Indexed: 11/15/2022] Open
Abstract
Early-stage non-small cell lung cancer (NSCLC) patients are at substantial risk of poor prognosis. We attempted to develop a reliable metabolic gene-set-based signature that can predict prognosis accurately for early-stage patients. Least absolute shrinkage and selection operator method Cox regression models were performed to filter the most useful prognostic genes, and a metabolic gene-set-based signature was constructed. Forty-two metabolism-related genes were finally identified, and with specific risk score formula, patients were classified into high-risk and low-risk groups. Overall survival was significantly different between the two groups in discovery (HR: 5.050, 95% CI: 3.368-7.574, P < 0.001), internal validation series (HR: 6.044, 95% CI: 3.918-9.322, P < 0.001), GSE30219 (HR: 2.059, 95% CI: 1.510-2.808, P < 0.001), and GSE68456 (HR: 2.448, 95% CI: 1.723-3.477, P < 0.001). Survival receiver operating characteristic curve at the 5 years suggested that the metabolic signature (area under the curve [AUC] = 0.805) had better prognostic accuracy than any other clinicopathological factors. Further analysis revealed the distinct differences in immune cell infiltration and tumor purity reflected by an immune and stromal score between high- and low-risk patients. In conclusion, the novel metabolic signature developed in our study shows robust prognostic accuracy in predicting prognosis for early-stage NSCLC patients and may function as a reliable marker for guiding more effective immunotherapy strategies.
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Affiliation(s)
- Jing Li
- Department of CyberKnife Center, Huashan Hospital, Fudan University, No. 525, Hongfeng Road, Pudong District, Shanghai 200040, China
| | - Yun Guan
- Department of CyberKnife Center, Huashan Hospital, Fudan University, No. 525, Hongfeng Road, Pudong District, Shanghai 200040, China
| | - Rongrong Zhu
- Department of Rehabilitation, Northern Jiangsu People's Hospital, Yangzhou, 225001, China
| | - Yang Wang
- Department of CyberKnife Center, Huashan Hospital, Fudan University, No. 525, Hongfeng Road, Pudong District, Shanghai 200040, China
| | - Huaguang Zhu
- Department of CyberKnife Center, Huashan Hospital, Fudan University, No. 525, Hongfeng Road, Pudong District, Shanghai 200040, China
| | - Xin Wang
- Department of CyberKnife Center, Huashan Hospital, Fudan University, No. 525, Hongfeng Road, Pudong District, Shanghai 200040, China
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22
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Murphy RG, Gilmore A, Senevirathne S, O'Reilly PG, LaBonte Wilson M, Jain S, McArt DG. Particle Swarm Optimization Artificial Intelligence technique for gene signature discovery in transcriptomic cohorts. Comput Struct Biotechnol J 2022; 20:5547-5563. [PMID: 36249564 PMCID: PMC9556859 DOI: 10.1016/j.csbj.2022.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/12/2022] Open
Abstract
EBPSO identifies unique, accurate, and succinct gene signatures. Key genes within the signatures provide biological insights its associated functions. A web-based micro-framework developed for ease of use and real-time visualizations. A promising alternative to traditional single gene signature generation. Downstream analysis will better translate these signatures towards clinical translation.
The development of gene signatures is key for delivering personalized medicine, despite only a few signatures being available for use in the clinic for cancer patients. Gene signature discovery tends to revolve around identifying a single signature. However, it has been shown that various highly predictive signatures can be produced from the same dataset. This study assumes that the presentation of top ranked signatures will allow greater efforts in the selection of gene signatures for validation on external datasets and for their clinical translation. Particle swarm optimization (PSO) is an evolutionary algorithm often used as a search strategy and largely represented as binary PSO (BPSO) in this domain. BPSO, however, fails to produce succinct feature sets for complex optimization problems, thus affecting its overall runtime and optimization performance. Enhanced BPSO (EBPSO) was developed to overcome these shortcomings. Thus, this study will validate unique candidate gene signatures for different underlying biology from EBPSO on transcriptomics cohorts. EBPSO was consistently seen to be as accurate as BPSO with substantially smaller feature signatures and significantly faster runtimes. 100% accuracy was achieved in all but two of the selected data sets. Using clinical transcriptomics cohorts, EBPSO has demonstrated the ability to identify accurate, succinct, and significantly prognostic signatures that are unique from one another. This has been proposed as a promising alternative to overcome the issues regarding traditional single gene signature generation. Interpretation of key genes within the signatures provided biological insights into the associated functions that were well correlated to their cancer type.
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23
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Liang Y, Zhang X, Ma C, Hu J. m 6A Methylation Regulators Are Predictive Biomarkers for Tumour Metastasis in Prostate Cancer. Cancers (Basel) 2022; 14:cancers14164035. [PMID: 36011028 PMCID: PMC9406868 DOI: 10.3390/cancers14164035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Recurrence and metastatic progression always lead to dismal outcomes in prostate cancer (PCa). There is no reliable biomarker for the prediction of recurrence and metastasis other than the Prostate Cancer Antigen (PCA). N6-methyladenosine (m6A) is the most common post-transcriptional mRNA modification and is regulated by m6A regulators dynamically. Since m6A modification is associated with cancer development and outgrowth, we performed a consensus clustering on PCa with regard to the gene expression of all m6A regulators. We identified three subtypes of Pca with distinct m6A expression patterns and enriched biological pathways. We also established an m6A score for metastasis prediction based on our clustering, which is potentially a predictive biomarker for Pca metastasis. Abstract Prostate cancer (PCa) is one of the most common cancers in men. Usually, most PCas at initial diagnosis are localized and hormone-dependent, and grow slowly. Patients with localized PCas have a nearly 100% 5-year survival rate; however, the 5-year survival rate of metastatic or progressive PCa is still dismal. N6-methyladenosine (m6A) is the most common post-transcriptional mRNA modification and is dynamically regulated by m6A regulators. A few studies have shown that the abnormal expression of m6A regulators is significantly associated with cancer progression and immune cell infiltration, but the roles of these regulators in PCa remain unclear. Here, we examined the expression profiles and methylation levels of 21 m6A regulators across the Cancer Genome Atlas (TCGA), 495 PCas by consensus clustering, and correlated the expression of m6A regulators with PCa progression and immune cell infiltration. Consensus clustering was applied for subtyping Pca samples into clusters based on the expression profiles of m6A regulators. Each subtype’s signature genes were obtained by a pairwise differential expression analysis. Featured pathways of m6A subtypes were predicted by Gene Ontology. The m6A score was developed to predict m6A activation. The association of the m6A score with patients’ survival, metastasis and immune cell infiltration was also investigated. We identified three distinct clusters in PCa based on the expression profiles of 21 m6A regulators by consensus clustering. The differential expression and pathway analyses on the three clusters uncovered the m6A regulators involved in metabolic processes and immune responses in PCa. Moreover, we developed an m6A score to evaluate the m6A regulator activation for PCa. The m6A score is significantly associated with Gleason scores and metastasis in PCa. The predictive capacity of the m6A score on PCa metastasis was also validated in another independent cohort with an area under the curve of 89.5%. Hence, our study revealed the critical role of m6A regulators in PCa progression and the m6A score is a promising predictive biomarker for PCa metastasis.
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Affiliation(s)
- Yingchun Liang
- Department of Urology, Huashan Hospital, Fudan University, No. 12 WuLuMuQi Middle Road, Shanghai 200040, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaohua Zhang
- Department of Urology, Huashan Hospital, Fudan University, No. 12 WuLuMuQi Middle Road, Shanghai 200040, China
| | - Chenkai Ma
- Molecular Diagnostic Solution, Nutrition and Health, Health and Biosecurity, CSIRO, North Ryde 2113, Australia
- Correspondence: (C.M.); (J.H.)
| | - Jimeng Hu
- Department of Urology, Huashan Hospital, Fudan University, No. 12 WuLuMuQi Middle Road, Shanghai 200040, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Correspondence: (C.M.); (J.H.)
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24
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Liu Y, Wang T, Li R. A prognostic Risk Score model for oral squamous cell carcinoma constructed by 6 glycolysis-immune-related genes. BMC Oral Health 2022; 22:324. [PMID: 35922788 PMCID: PMC9351085 DOI: 10.1186/s12903-022-02358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/26/2022] [Indexed: 12/23/2022] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is the most frequent tumor of the head and neck. The glycolysis-related genes and immune-related genes have been proven prognostic values in various cancers. Our study aimed to test the prognostic value of glycolysis-immune-related genes in OSCC. Methods Data of OSCC patients were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Enrichment analysis was applied to the glycolysis- and immune-related genes screened by differential expression analysis. Univariate Cox and LASSO Cox analyses were used to filtrate the genes related to the prognosis of OSCC and to construct Risk Score model. Results A Risk Score model was constructed by six glycolysis-immune-related genes (including ALDOC, VEGFA, HRG, PADI3, IGSF11 and MIPOL1). High risk OSCC patients (Risk Score >−0.3075) had significantly worse overall survival than that of low risk patients (Risk Score <−0.3075). Conclusions The Risk Score model constructed basing on 6 glycolysis-immune-related genes was reliable in stratifying OSCC patients with different prognosis.
Supplementary Information The online version contains supplementary material available at 10.1186/s12903-022-02358-0.
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Affiliation(s)
- Yi Liu
- Department of Stomatology, Tianjin First Central Hospital, Nankai District, No.24 Fukang Road, Tianjin, 300192, People's Republic of China.
| | - Tong Wang
- Department of Stomatology, Tianjin First Central Hospital, Nankai District, No.24 Fukang Road, Tianjin, 300192, People's Republic of China
| | - Ronghua Li
- Department of Stomatology, Tianjin First Central Hospital, Nankai District, No.24 Fukang Road, Tianjin, 300192, People's Republic of China
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25
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Sutera P, Deek MP, Van der Eecken K, Wyatt AW, Kishan AU, Molitoris JK, Ferris MJ, Minhaj Siddiqui M, Rana Z, Mishra MV, Kwok Y, Davicioni E, Spratt DE, Ost P, Feng FY, Tran PT. Genomic biomarkers to guide precision radiotherapy in prostate cancer. Prostate 2022; 82 Suppl 1:S73-S85. [PMID: 35657158 PMCID: PMC9202472 DOI: 10.1002/pros.24373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/30/2022] [Accepted: 04/29/2022] [Indexed: 11/08/2022]
Abstract
Our ability to prognosticate the clinical course of patients with cancer has historically been limited to clinical, histopathological, and radiographic features. It has long been clear however, that these data alone do not adequately capture the heterogeneity and breadth of disease trajectories experienced by patients. The advent of efficient genomic sequencing has led to a revolution in cancer care as we try to understand and personalize treatment specific to patient clinico-genomic phenotypes. Within prostate cancer, emerging evidence suggests that tumor genomics (e.g., DNA, RNA, and epigenetics) can be utilized to inform clinical decision making. In addition to providing discriminatory information about prognosis, it is likely tumor genomics also hold a key in predicting response to oncologic therapies which could be used to further tailor treatment recommendations. Herein we review select literature surrounding the use of tumor genomics within the management of prostate cancer, specifically leaning toward analytically validated and clinically tested genomic biomarkers utilized in radiotherapy and/or adjunctive therapies given with radiotherapy.
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Affiliation(s)
- Philip Sutera
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew P. Deek
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Kim Van der Eecken
- Department of Pathology, Ghent University Hospital, Cancer Research Institute (CRIG), Ghent, Belgium
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amar U. Kishan
- Department of Radiation Oncology, UCLA, Los Angeles, CA, USA
| | - Jason K. Molitoris
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew J. Ferris
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - M. Minhaj Siddiqui
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zaker Rana
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark V. Mishra
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Young Kwok
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Daniel E. Spratt
- Department of Radiation Oncology, University Hospitals, Cleveland, OH, USA
| | - Piet Ost
- Department of Radiation Oncology, Iridium Network, Antwerp, Belgium and Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Felix Y. Feng
- Departments of Radiation Oncology, Medicine and Urology, UCSF, San Francisco, CA, USA
| | - Phuoc T. Tran
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
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Smith TAD, Lane B, More E, Valentine H, Lunj S, Abdelkarem OA, Irlam-Jones J, Shabbir R, Vora S, Denley H, Reeves KJ, Hoskin PJ, Choudhury A, West CML. Comparison of multiple gene expression platforms for measuring a bladder cancer hypoxia signature. Mol Med Rep 2022; 26:261. [PMID: 35730624 DOI: 10.3892/mmr.2022.12777] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/25/2022] [Indexed: 11/05/2022] Open
Abstract
Tumour hypoxia status provides prognostic information and predicts response to hypoxia‑modifying treatments. A previous study by our group derived a 24‑gene signature to assess hypoxia in bladder cancer. The objectives of the present study were to compare platforms for generating signature scores, identify cut‑off values for prospective studies, assess intra‑tumour heterogeneity and confirm hypoxia relevance. Briefly, RNA was extracted from prospectively collected diagnostic biopsies of muscle invasive bladder cancer (51 patients), and gene expression was measured using customised Taqman Low Density Array (TLDA) cards, NanoString and Clariom S arrays. Cross‑platform transferability of the gene signature was assessed using regression and concordance analysis. The cut‑off values were the cohort median expression values. Intra‑ and inter‑tumour variability were determined in a retrospective patient cohort (n=51) with multiple blocks (2‑18) from the same tumour. To demonstrate relevance, bladder cancer cell lines were exposed to hypoxia (0.1% oxygen, 24 h), and extracted RNA was run on custom TLDA cards. Hypoxia scores (HS) values showed good agreement between platforms: Clariom S vs. TLDA (r=0.72, P<0.0001; concordance 73%); Clariom S vs. NanoString (r=0.84, P<0.0001; 78%); TLDA vs. NanoString (r=0.80, P<0.0001; 78%). Cut‑off values were 0.047 (TLDA), 7.328 (NanoString) and 6.667 (Clariom S). Intra‑tumour heterogeneity in gene expression and HS (coefficient of variation 3.9%) was less than inter‑tumour (7.9%) variability. HS values were higher in bladder cancer cells exposed to hypoxia compared with normoxia (P<0.02). In conclusion, the present study revealed that application of the 24‑gene bladder cancer hypoxia signature was platform agnostic, cut‑off values determined prospectively can be used in a clinical trial, intra‑tumour heterogeneity was low and the signature was sensitive to changes in oxygen levels in vitro.
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Affiliation(s)
- Tim A D Smith
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Brian Lane
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Elisabet More
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Helen Valentine
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Sapna Lunj
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Omneya A Abdelkarem
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria 21561, Egypt
| | - J Irlam-Jones
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Rekaya Shabbir
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Shrushti Vora
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Helen Denley
- Pathology Centre, Shrewsbury and Telford NHS Trust, Royal Shrewsbury Hospital, Shrewsbury SY3 8XQ, UK
| | - Kimberley J Reeves
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Peter J Hoskin
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
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Sun Q, Wang H, Xiao B, Xue D, Wang G. Development and Validation of a 6-Gene Hypoxia-Related Prognostic Signature For Cholangiocarcinoma. Front Oncol 2022; 12:954366. [PMID: 35924146 PMCID: PMC9339701 DOI: 10.3389/fonc.2022.954366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022] Open
Abstract
Cholangiocarcinoma (CHOL) is highly malignant and has a poor prognosis. This study is committed to creating a new prognostic model based on hypoxia related genes. Here, we established a novel tumor hypoxia-related prognostic model consisting of 6 hypoxia-related genes by univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) algorithm to predict CHOL prognosis and then the risk score for each patient was calculated. The results showed that the patients with high-risk scores had poor prognosis compared with those with low-risk scores, which was verified as an independent predictor by multivariate analysis. The hypoxia-related prognostic model was validated in both TCGA and GEO cohorts and exhibited excellent performance in predicting overall survival in CHOL. The PPI results suggested that hypoxia-related genes involved in the model may play a central role in regulating the hypoxic state. In addition, the presence of IDH1 mutations in the high-risk group was high, and GSEA results showed that some metabolic pathways were upregulated, but immune response processes were generally downregulated. These factors may be potential reasons for the high-risk group with worse prognosis. The analysis of different immune regulation-related processes in the high- and low-risk groups revealed that the expression of genes related to immune checkpoints would show differences between these two groups. We further verified the expression of the oncogene PPFIA4 in the model, and found that compared with normal samples, CHOL patients were generally highly expressed, and the patients with high-expression of PPFIA4 had a poor prognosis. In summary, the present study may provide a valid prognostic model for bile duct cancer to inform better clinical management of patients.
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Affiliation(s)
- Qi Sun
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Huxia Wang
- Mammary Department, Shaanxi Provincial Cancer Hospital, Xi’an, China
| | - Baoan Xiao
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Dong Xue
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Guanghui Wang
- Department of General Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Guanghui Wang,
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Guo J, Zhao C, Zhang X, Wan Z, Chen T, Miao J, Cai J, Xie W, Chen H, Huang M, Zhao X, Wei W, Shen Q. A novel 8-gene panel for prediction of early biochemical recurrence in patients with prostate cancer after radical prostatectomy. Am J Cancer Res 2022; 12:3318-3332. [PMID: 35968320 PMCID: PMC9360249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023] Open
Abstract
Approximately 25% of prostate cancer (PCa) cases experience biochemical recurrence (BCR) following radical prostatectomy (RP). The patients with BCR, especially with BCR ≤2 year after RP (early BCR), are more likely to develop clinical metastasis and castration resistance. Now decision-making regarding BCR after RP relies solely on clinical parameters. We thus attempted to establish an early BCR-risk prediction model by combining a molecular signature with clinicopathological features for guiding clinical decision-making. In this study, an 8-gene signature was derived, and these eight genes were SPTBN2, LGI3, TGM3, LENG9, HAS3, SLC25A27, PCDHGA1, and ADPRHL1. The Kaplan-Meier analysis revealed a significantly prolonged BCR-free survival in the patients with low-risk scores compared to those with high-risk scores in both training and validation datasets. Harrell's concordance index and time-dependent receiver operating characteristic analysis demonstrated that this gene signature tended to outperform three commercial panels at early BCR prediction. Moreover, this signature was also proven as an independent predictor of BCR-free survival. A nomogram, incorporating the gene signature and clinicopathologic features, was constructed and excellently predicted 1-, 2- and 3-year BCR-free survival of localized PCa patients after RP. Gene set enrichment analysis, tumor immunity, and mRNA expression profiling analysis showed that the high-risk group was more prone to the immunosuppressive microenvironment and impaired DNA damage response than the low-risk group. Collectively, we successfully developed a novel 8-gene signature as a powerful predictor for early BCR after RP and created a prognostic nomogram, which may help inform the clinical management of PCa.
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Affiliation(s)
- Jinan Guo
- Department of Urology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, The First Affiliated Hospital of South University of Science and Technology of ChinaShenzhen, China
- Shenzhen Urology Minimally Invasive Engineering CenterShenzhen, China
| | - Chenhui Zhao
- Ruijin Hospital Lu Wan Branch, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Xinzhou Zhang
- Department of Nephrology, Shenzhen key Laboratory of Kindey Diseases, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, The First Affiliated Hospital of South University of Science and Technology of ChinaShenzhen, China
| | - Zhong Wan
- Shuguang Hospital, Shanghai University of Traditional Chinese MedicineShanghai, China
| | | | | | | | | | - Hao Chen
- 3D Medicines, IncShanghai, China
| | | | | | - Wei Wei
- Department of Urology, Hwa Mei Hospital, University of Chinese Academy of SciencesNingbo, China
| | - Qi Shen
- Department of Hematology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, The First Affiliated Hospital of South University of Science and Technology of ChinaShenzhen, China
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Gallez B. The Role of Imaging Biomarkers to Guide Pharmacological Interventions Targeting Tumor Hypoxia. Front Pharmacol 2022; 13:853568. [PMID: 35910347 PMCID: PMC9335493 DOI: 10.3389/fphar.2022.853568] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/23/2022] [Indexed: 12/12/2022] Open
Abstract
Hypoxia is a common feature of solid tumors that contributes to angiogenesis, invasiveness, metastasis, altered metabolism and genomic instability. As hypoxia is a major actor in tumor progression and resistance to radiotherapy, chemotherapy and immunotherapy, multiple approaches have emerged to target tumor hypoxia. It includes among others pharmacological interventions designed to alleviate tumor hypoxia at the time of radiation therapy, prodrugs that are selectively activated in hypoxic cells or inhibitors of molecular targets involved in hypoxic cell survival (i.e., hypoxia inducible factors HIFs, PI3K/AKT/mTOR pathway, unfolded protein response). While numerous strategies were successful in pre-clinical models, their translation in the clinical practice has been disappointing so far. This therapeutic failure often results from the absence of appropriate stratification of patients that could benefit from targeted interventions. Companion diagnostics may help at different levels of the research and development, and in matching a patient to a specific intervention targeting hypoxia. In this review, we discuss the relative merits of the existing hypoxia biomarkers, their current status and the challenges for their future validation as companion diagnostics adapted to the nature of the intervention.
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Signature for Prostate Cancer Based on Autophagy-Related Genes and a Nomogram for Quantitative Risk Stratification. DISEASE MARKERS 2022; 2022:7598942. [PMID: 35860692 PMCID: PMC9293571 DOI: 10.1155/2022/7598942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022]
Abstract
Background. Prostate cancer (PCa) ranks as the most common malignancy and the second leading cause of cancer-related death among males worldwide. The essential role of autophagy in the progression of PCa and treatment resistance has been preliminarily revealed. However, comprehensive molecular elucidations of the correlation between PCa and autophagy are rare. Method. We obtained transcription information and corresponding clinicopathological profiles of PCa patients from TCGA, MSKCC, and GEO datasets. LAASO analysis was employed to select gene signatures and estimate the autophagy score for each patient. Correlations between the signature and prognosis of PCa were investigated by K-M and multivariate Cox regression analyses. A nomogram was established on the basis of the above results. Further validations relied on ROC, calibration analysis, decision curve analysis, and external cohorts. Variable activated signaling pathways were revealed using GSVA algorithms, and the genetic alteration landscape was elucidated via the oncodrive module from the “maftools” R package. In addition, we also examined the therapeutic role of the signature based on phenotype data from GDSC 2016. Result. Six autophagy-related genes were eventually selected to establish the signature, including ULK1, CAPN10, FKBP5, UBE2T, NLRC4, and BNIP3L. We used these genes and corresponding coefficients to calculate an autophagy score (AutS) for each patient in this study. A high AutS group and a low AutS group were divided on the mean AutS of the patients. Longer overall survival, higher Gleason score and PSA, and better response to ADT were observed in patients with high AutS. Meanwhile, we found that high AutS PCa was related to more proliferation-associated signaling activation and higher genetic mutation frequencies, manifesting a poor prognosis. A nomogram was constructed based on GS, T stage, PSA, and AutS as covariates. Its discriminative efficacy and clinical value were validated using robust statistical methods. Finally, we tested its prognostic value through two external cohorts and six published signatures. Conclusion. The autophagy-related gene signature is a highly discriminative model for risk stratification and drug therapy in PCa, and a nomogram incorporating AutS might be a promising tool for precision medicine.
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Liu L, Zhu H, Wang P, Wu S. Construction of a Six-Gene Prognostic Risk Model Related to Hypoxia and Angiogenesis for Cervical Cancer. Front Genet 2022; 13:923263. [PMID: 35769999 PMCID: PMC9234147 DOI: 10.3389/fgene.2022.923263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/25/2022] [Indexed: 12/24/2022] Open
Abstract
Background: The prognosis of cervical cancer (CC) is poor and not accurately reflected by the primary tumor node metastasis staging system. Our study aimed to develop a novel survival-prediction model. Methods: Hallmarks of CC were quantified using single-sample gene set enrichment analysis and univariate Cox proportional hazards analysis. We linked gene expression, hypoxia, and angiogenesis using weighted gene co-expression network analysis (WGCNA). Univariate and multivariate Cox regression was combined with the random forest algorithm to construct a prognostic model. We further evaluated the survival predictive power of the gene signature using Kaplan-Meier analysis and receiver operating characteristic (ROC) curves. Results: Hypoxia and angiogenesis were the leading risk factors contributing to poor overall survival (OS) of patients with CC. We identified 109 candidate genes using WGCNA and univariate Cox regression. Our established prognostic model contained six genes (MOCSI, PPP1R14A, ESM1, DES, ITGA5, and SERPINF1). Kaplan-Meier analysis indicated that high-risk patients had worse OS (hazard ratio = 4.63, p < 0.001). Our model had high predictive power according to the ROC curve. The C-index indicated that the risk score was a better predictor of survival than other clinicopathological variables. Additionally, univariate and multivariate Cox regressions indicated that the risk score was the only independent risk factor for poor OS. The risk score was also an independent predictor in the validation set (GSE52903). Bivariate survival prediction suggested that patients exhibited poor prognosis if they had high z-scores for hypoxia or angiogenesis and high risk scores. Conclusions: We established a six-gene survival prediction model associated with hypoxia and angiogenesis. This novel model accurately predicts survival and also provides potential therapeutic targets.
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Affiliation(s)
- Lili Liu
- TCM Gynecology Department, Foshan Fosun Chancheng Hospital, Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
| | - Hongcang Zhu
- Foshan Retirement Center for Retired Cadres, Guangdong Military Region of the PLA, Foshan, China
| | - Pei Wang
- Foshan Clinical Medical School, Guangzhou University of Chinese Medicine, Foshan, China
| | - Suzhen Wu
- TCM Gynecology Department, Foshan Fosun Chancheng Hospital, Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, China
- *Correspondence: Suzhen Wu,
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Burns D, Anokian E, Saunders EJ, Bristow RG, Fraser M, Reimand J, Schlomm T, Sauter G, Brors B, Korbel J, Weischenfeldt J, Waszak SM, Corcoran NM, Jung CH, Pope BJ, Hovens CM, Cancel-Tassin G, Cussenot O, Loda M, Sander C, Hayes VM, Dalsgaard Sorensen K, Lu YJ, Hamdy FC, Foster CS, Gnanapragasam V, Butler A, Lynch AG, Massie CE, Woodcock DJ, Cooper CS, Wedge DC, Brewer DS, Kote-Jarai Z, Eeles RA. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. Eur Urol 2022; 82:201-211. [PMID: 35659150 DOI: 10.1016/j.eururo.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Germline variants explain more than a third of prostate cancer (PrCa) risk, but very few associations have been identified between heritable factors and clinical progression. OBJECTIVE To find rare germline variants that predict time to biochemical recurrence (BCR) after radical treatment in men with PrCa and understand the genetic factors associated with such progression. DESIGN, SETTING, AND PARTICIPANTS Whole-genome sequencing data from blood DNA were analysed for 850 PrCa patients with radical treatment from the Pan Prostate Cancer Group (PPCG) consortium from the UK, Canada, Germany, Australia, and France. Findings were validated using 383 patients from The Cancer Genome Atlas (TCGA) dataset. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS A total of 15,822 rare (MAF <1%) predicted-deleterious coding germline mutations were identified. Optimal multifactor and univariate Cox regression models were built to predict time to BCR after radical treatment, using germline variants grouped by functionally annotated gene sets. Models were tested for robustness using bootstrap resampling. RESULTS AND LIMITATIONS Optimal Cox regression multifactor models showed that rare predicted-deleterious germline variants in "Hallmark" gene sets were consistently associated with altered time to BCR. Three gene sets had a statistically significant association with risk-elevated outcome when modelling all samples: PI3K/AKT/mTOR, Inflammatory response, and KRAS signalling (up). PI3K/AKT/mTOR and KRAS signalling (up) were also associated among patients with higher-grade cancer, as were Pancreas-beta cells, TNFA signalling via NKFB, and Hypoxia, the latter of which was validated in the independent TCGA dataset. CONCLUSIONS We demonstrate for the first time that rare deleterious coding germline variants robustly associate with time to BCR after radical treatment, including cohort-independent validation. Our findings suggest that germline testing at diagnosis could aid clinical decisions by stratifying patients for differential clinical management. PATIENT SUMMARY Prostate cancer patients with particular genetic mutations have a higher chance of relapsing after initial radical treatment, potentially providing opportunities to identify patients who might need additional treatments earlier.
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Affiliation(s)
| | | | | | - Robert G Bristow
- Manchester Cancer Research Centre and CRUK Manchester Institute, The University of Manchester, Manchester, UK
| | - Michael Fraser
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada; Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics & Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Guido Sauter
- University Medical Centre Hamburg - Eppendorf, Hamburg, Germany
| | - Benedikt Brors
- German Cancer Research Center (DKFZ), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Jan Korbel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim Weischenfeldt
- Charité - Universitätsmedizin Berlin, Berlin, Germany; Biotech Research & Innovation Centre (BRIC) & Finsen Laboratory, University of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Niall M Corcoran
- Department of Surgery, The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Grattan Street, Victoria, Australia
| | - Chol-Hee Jung
- The University of Melbourne, Grattan Street, Parkville, Victoria, Australia
| | - Bernard J Pope
- Department of Surgery, The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; Royal Melbourne Hospital, Melbourne, Parwille, Victoria, Australia
| | - Chris M Hovens
- Melbourne Bioinformatics, The University of Melbourne, Grattan Street, Victoria, Australia; The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, The Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Géraldine Cancel-Tassin
- CeRePP, Hopital Tenon, Paris, France; Sorbonne Universite, GRC n°5 Predictive Onco-Urology, APHP, Tenon Hospital, Paris, France
| | - Olivier Cussenot
- CeRePP, Hopital Tenon, Paris, France; Sorbonne Universite, GRC n°5 Predictive Onco-Urology, APHP, Tenon Hospital, Paris, France
| | - Massimo Loda
- Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia; School of Medical Sciences, University of Sydney, Charles Perkins Centre, Camperdown, NSW, Australia
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark; Department of Clinical Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Yong-Jie Lu
- Centre for Biomarker and Therapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | | | | | - Adam Butler
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Andy G Lynch
- School of Medicine, University of St Andrews, St Andrews, Fife, UK; School of Mathematics & Statistics, St Andrews, Fife, UK
| | - Charlie E Massie
- CRUK Cambridge Institute, Hutchison MRC Research Centre, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
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- CR-UK/Prostate Cancer UK, ICGC, The Pan Prostate Cancer Group, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - David C Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
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Li R, Zhu J, Zhong W, Jia Z. Comprehensive evaluation of machine learning models and gene expression signatures for prostate cancer prognosis using large population cohorts. Cancer Res 2022; 82:1832-1843. [PMID: 35358302 DOI: 10.1158/0008-5472.can-21-3074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/07/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022]
Abstract
Overtreatment remains a pervasive problem in prostate cancer (PCa) management due to the highly variable and often indolent course of disease. Molecular signatures derived from gene expression profiling have played critical roles in guiding PCa treatment decisions. Many gene expression signatures have been developed to improve the risk stratification of PCa and some of them have already been applied to clinical practice. However, no comprehensive evaluation has been performed to compare the performance of these signatures. In this study, we conducted a systematic and unbiased evaluation of 15 machine learning (ML) algorithms and 30 published PCa gene expression-based prognostic signatures leveraging 10 transcriptomics datasets with 1,558 primary PCa patients from public data repositories. This analysis revealed that survival analysis models outperformed binary classification models for risk assessment, and the performance of the survival analysis methods - Cox model regularized with ridge penalty (Cox-Ridge) and partial least squares regression for Cox model (Cox-PLS) - were generally more robust than the other methods. Based on the Cox-Ridge algorithm, several top prognostic signatures displayed comparable or even better performance than commercial panels. These findings will facilitate the identification of existing prognostic signatures that are promising for further validation in prospective studies and promote the development of robust prognostic models to guide clinical decision-making. Moreover, this study provides a valuable data resource from large primary PCa cohorts, which can be used to develop, validate, and evaluate novel statistical methodologies and molecular signatures to improve PCa management.
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Affiliation(s)
- Ruidong Li
- University of California, Riverside, Riveside, United States
| | - Jianguo Zhu
- Guizhou Provincial People's Hospital, GuiYang, Guizhou, China
| | - Weide Zhong
- Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Zhenyu Jia
- University of California of Riverside, Riverside, California, United States
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A prognostic hypoxia gene signature with low heterogeneity within the dominant tumour lesion in prostate cancer patients. Br J Cancer 2022; 127:321-328. [PMID: 35332267 PMCID: PMC9296675 DOI: 10.1038/s41416-022-01782-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/10/2022] [Accepted: 03/08/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Gene signatures measured in a biopsy have been proposed as hypoxia biomarkers in prostate cancer. We assessed a previously developed signature, and aimed to determine its relationship to hypoxia and its heterogeneity within the dominant (index) lesion of prostate cancer. METHODS The 32-gene signature was assessed from gene expression data of 141 biopsies from the index lesion of 94 patients treated with prostatectomy. A gene score calculated from the expression levels was applied in the analyses. Hypoxic fraction from pimonidazole immunostained whole-mount and biopsy sections was used as reference standard for hypoxia. RESULTS The gene score was correlated with pimonidazole-defined hypoxic fraction in whole-mount sections, and the two parameters showed almost equal association with clinical markers of tumour aggressiveness. Based on the gene score, incorrect classification according to hypoxic fraction in whole-mount sections was seen in one third of the patients. The incorrect classifications were apparently not due to intra-tumour heterogeneity, since the score had low heterogeneity compared to pimonidazole-defined hypoxic fraction in biopsies. The score showed prognostic significance in uni-and multivariate analysis in independent cohorts. CONCLUSIONS Our signature from the index lesion reflects tumour hypoxia and predicts prognosis in prostate cancer, independent of intra-tumour heterogeneity in pimonidazole-defined hypoxia.
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Risk subtyping and prognostic assessment of prostate cancer based on consensus genes. Commun Biol 2022; 5:233. [PMID: 35293897 PMCID: PMC8924191 DOI: 10.1038/s42003-022-03164-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 02/14/2022] [Indexed: 01/20/2023] Open
Abstract
Prostate cancer (PCa) is the most frequent malignancy in male urogenital system around worldwide. We performed molecular subtyping and prognostic assessment based on consensus genes in patients with PCa. Five cohorts containing 1,046 PCa patients with RNA expression profiles and recorded clinical follow-up information were included. Univariate, multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) Cox regression were used to select prognostic genes and establish the signature. Immunohistochemistry staining, cell proliferation, migration and invasion assays were used to assess the biological functions of key genes. Thirty-nine intersecting consensus prognostic genes from five independent cohorts were identified. Subsequently, an eleven-consensus-gene classifier was established. In addition, multivariate Cox regression analyses showed that the classifier served as an independent indicator of recurrence-free survival in three of the five cohorts. Combined receiver operating characteristic (ROC) analysis achieved synthesized effects by combining the classifier with clinicopathological features in four of five cohorts. SRD5A2 inhibits cell proliferation, while ITGA11 promotes cell migration and invasion, possibly through the PI3K/AKT signaling pathway. To conclude, we established and validated an eleven-consensus-gene classifier, which may add prognostic value to the currently available staging system. By analysis of gene expression profiles of prostate cancer patients from multiple platforms, an eleven-consensus-gene classifier is constructed to provide a robust tool for the prediction of recurrence-free survival.
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Ryniawec JM, Coope MR, Loertscher E, Bageerathan V, de Oliveira Pessoa D, Warfel NA, Cress AE, Padi M, Rogers GC. GLUT3/SLC2A3 Is an Endogenous Marker of Hypoxia in Prostate Cancer Cell Lines and Patient-Derived Xenograft Tumors. Diagnostics (Basel) 2022; 12:diagnostics12030676. [PMID: 35328229 PMCID: PMC8946944 DOI: 10.3390/diagnostics12030676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 01/17/2023] Open
Abstract
The microenvironment of solid tumors is dynamic and frequently contains pockets of low oxygen levels (hypoxia) surrounded by oxygenated tissue. Indeed, a compromised vasculature is a hallmark of the tumor microenvironment, creating both spatial gradients and temporal variability in oxygen availability. Notably, hypoxia associates with increased metastasis and poor survival in patients. Therefore, to aid therapeutic decisions and better understand hypoxia’s role in cancer progression, it is critical to identify endogenous biomarkers of hypoxia to spatially phenotype oncogenic lesions in human tissue, whether precancerous, benign, or malignant. Here, we characterize the glucose transporter GLUT3/SLC2A3 as a biomarker of hypoxic prostate epithelial cells and prostate tumors. Transcriptomic analyses of non-tumorigenic, immortalized prostate epithelial cells revealed a highly significant increase in GLUT3 expression under hypoxia. Additionally, GLUT3 protein increased 2.4-fold in cultured hypoxic prostate cell lines and was upregulated within hypoxic regions of xenograft tumors, including two patient-derived xenografts (PDX). Finally, GLUT3 out-performs other established hypoxia markers; GLUT3 staining in PDX specimens detects 2.6–8.3 times more tumor area compared to a mixture of GLUT1 and CA9 antibodies. Therefore, given the heterogeneous nature of tumors, we propose adding GLUT3 to immunostaining panels when trying to detect hypoxic regions in prostate samples.
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Affiliation(s)
- John M. Ryniawec
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA; (J.M.R.); (M.R.C.); (E.L.); (N.A.W.)
| | - Matthew R. Coope
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA; (J.M.R.); (M.R.C.); (E.L.); (N.A.W.)
| | - Emily Loertscher
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA; (J.M.R.); (M.R.C.); (E.L.); (N.A.W.)
| | - Vignesh Bageerathan
- Biostatistics and Bioinformatics Shared Resource, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (V.B.); (D.d.O.P.)
| | - Diogo de Oliveira Pessoa
- Biostatistics and Bioinformatics Shared Resource, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (V.B.); (D.d.O.P.)
| | - Noel A. Warfel
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA; (J.M.R.); (M.R.C.); (E.L.); (N.A.W.)
| | - Anne E. Cress
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA; (J.M.R.); (M.R.C.); (E.L.); (N.A.W.)
- Correspondence: (A.E.C.); (M.P.); (G.C.R.)
| | - Megha Padi
- Department of Molecular and Cellular Biology, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85721, USA
- Correspondence: (A.E.C.); (M.P.); (G.C.R.)
| | - Gregory C. Rogers
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85719, USA; (J.M.R.); (M.R.C.); (E.L.); (N.A.W.)
- Correspondence: (A.E.C.); (M.P.); (G.C.R.)
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Stoica SI, Bleotu C, Ciobanu V, Ionescu AM, Albadi I, Onose G, Munteanu C. Considerations about Hypoxic Changes in Neuraxis Tissue Injuries and Recovery. Biomedicines 2022; 10:481. [PMID: 35203690 PMCID: PMC8962344 DOI: 10.3390/biomedicines10020481] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/06/2022] [Accepted: 02/13/2022] [Indexed: 02/01/2023] Open
Abstract
Hypoxia represents the temporary or longer-term decrease or deprivation of oxygen in organs, tissues, and cells after oxygen supply drops or its excessive consumption. Hypoxia can be (para)-physiological-adaptive-or pathological. Thereby, the mechanisms of hypoxia have many implications, such as in adaptive processes of normal cells, but to the survival of neoplastic ones, too. Ischemia differs from hypoxia as it means a transient or permanent interruption or reduction of the blood supply in a given region or tissue and consequently a poor provision with oxygen and energetic substratum-inflammation and oxidative stress damages generating factors. Considering the implications of hypoxia on nerve tissue cells that go through different ischemic processes, in this paper, we will detail the molecular mechanisms by which such structures feel and adapt to hypoxia. We will present the hypoxic mechanisms and changes in the CNS. Also, we aimed to evaluate acute, subacute, and chronic central nervous hypoxic-ischemic changes, hoping to understand better and systematize some neuro-muscular recovery methods necessary to regain individual independence. To establish the link between CNS hypoxia, ischemic-lesional mechanisms, and neuro-motor and related recovery, we performed a systematic literature review following the" Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA") filtering method by interrogating five international medical renown databases, using, contextually, specific keywords combinations/"syntaxes", with supplementation of the afferent documentation through an amount of freely discovered, also contributive, bibliographic resources. As a result, 45 papers were eligible according to the PRISMA-inspired selection approach, thus covering information on both: intimate/molecular path-physiological specific mechanisms and, respectively, consequent clinical conditions. Such a systematic process is meant to help us construct an article structure skeleton giving a primary objective input about the assembly of the literature background to be approached, summarised, and synthesized. The afferent contextual search (by keywords combination/syntaxes) we have fulfilled considerably reduced the number of obtained articles. We consider this systematic literature review is warranted as hypoxia's mechanisms have opened new perspectives for understanding ischemic changes in the CNS neuraxis tissue/cells, starting at the intracellular level and continuing with experimental research to recover the consequent clinical-functional deficits better.
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Affiliation(s)
- Simona Isabelle Stoica
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila” (UMPCD), 020022 Bucharest, Romania; (S.I.S.); (A.M.I.)
- Teaching Emergency Hospital “Bagdasar-Arseni” (TEHBA), 041915 Bucharest, Romania
| | - Coralia Bleotu
- Stefan S. Nicolau Institute of Virology, 030304 Bucharest, Romania;
| | - Vlad Ciobanu
- Computer Science Department, Politehnica University of Bucharest (PUB), 060042 Bucharest, Romania;
| | - Anca Mirela Ionescu
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila” (UMPCD), 020022 Bucharest, Romania; (S.I.S.); (A.M.I.)
| | - Irina Albadi
- Teaching Emergency County Hospital “Sf. Apostol Andrei”, 900591 Constanta, Romania;
- Faculty of Medicine, “Ovidius” University of Constanta, 900470 Constanta, Romania
| | - Gelu Onose
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila” (UMPCD), 020022 Bucharest, Romania; (S.I.S.); (A.M.I.)
- Teaching Emergency Hospital “Bagdasar-Arseni” (TEHBA), 041915 Bucharest, Romania
| | - Constantin Munteanu
- Teaching Emergency Hospital “Bagdasar-Arseni” (TEHBA), 041915 Bucharest, Romania
- Department of Research, Romanian Association of Balneology, 022251 Bucharest, Romania
- Faculty of Medical Bioengineering, University of Medicine and Pharmacy “Grigore T. Popa”, 700115 Iasi, Romania
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38
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Tutzauer J, Sjöström M, Holmberg E, Karlsson P, Killander F, Leeb-Lundberg LMF, Malmström P, Niméus E, Fernö M, Jögi A. Breast cancer hypoxia in relation to prognosis and benefit from radiotherapy after breast-conserving surgery in a large, randomised trial with long-term follow-up. Br J Cancer 2022; 126:1145-1156. [PMID: 35140341 PMCID: PMC9023448 DOI: 10.1038/s41416-021-01630-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/17/2021] [Accepted: 11/03/2021] [Indexed: 12/21/2022] Open
Abstract
Background Breast-conserving surgery followed by radiotherapy is part of standard treatment for early-stage breast cancer. Hypoxia is common in cancer and may affect the benefit of radiotherapy. Cells adapt to hypoxic stress largely via the transcriptional activity of hypoxia-inducible factor (HIF)-1α. Here, we aim to determine whether tumour HIF-1α-positivity and hypoxic gene-expression signatures associated with the benefit of radiotherapy, and outcome. Methods Tumour HIF-1α-status and expression of hypoxic gene signatures were retrospectively analysed in a clinical trial where 1178 women with primary T1-2N0M0 breast cancer were randomised to receive postoperative radiotherapy or not and followed 15 years for recurrence and 20 years for breast cancer death. Results The benefit from radiotherapy was similar in patients with HIF-1α-positive and -negative primary tumours. Both ipsilateral and any breast cancer recurrence were more frequent in women with HIF-1α-positive primary tumours (hazard ratio, HR0–5 yrs1.9 [1.3–2.9], p = 0.003 and HR0–5 yrs = 2.0 [1.5–2.8], p < 0.0001). Tumour HIF-1α-positivity is also associated with increased breast cancer death (HR0–10 years 1.9 [1.2–2.9], p = 0.004). Ten of the 11 investigated hypoxic gene signatures correlated positively to HIF-1α-positivity, and 5 to increased rate/risk of recurrence. Conclusions The benefit of postoperative radiotherapy persisted in patients with hypoxic primary tumours. Patients with hypoxic primary breast tumours had an increased risk of recurrence and breast cancer death.
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Affiliation(s)
- Julia Tutzauer
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Martin Sjöström
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Erik Holmberg
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrika Killander
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | | | - Per Malmström
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Emma Niméus
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Division of Surgery, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.,Department of Surgery Malmö, Skåne University Hospital, Malmö, Sweden
| | - Mårten Fernö
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Annika Jögi
- Translational Cancer Research, Department of Laboratory Medicine, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden. .,Skåne University Hospital, Malmö, Sweden.
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Wu F, Xu J, Jin M, Jiang X, Li J, Li X, Chen Z, Nie J, Meng Z, Wang G. Development and Verification of a Hypoxic Gene Signature for Predicting Prognosis, Immune Microenvironment, and Chemosensitivity for Osteosarcoma. Front Mol Biosci 2022; 8:705148. [PMID: 35071320 PMCID: PMC8766725 DOI: 10.3389/fmolb.2021.705148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Objective: Hypoxic tumors contribute to local failure and distant metastases. Nevertheless, the molecular hallmarks of hypoxia remain ill-defined in osteosarcoma. Here, we developed a hypoxic gene signature in osteosarcoma prognoses. Methods: With the random survival forest algorithm, a prognostic hypoxia-related gene signature was constructed for osteosarcoma in the TARGET cohort. Overall survival (OS) analysis, receiver operating characteristic (ROC) curve, multivariate cox regression analysis, and subgroup analysis were utilized for assessing the predictive efficacy of this signature. Also, external validation was presented in the GSE21257 cohort. GSEA was applied for signaling pathways involved in the high- and low-risk samples. Correlation analyses between risk score and immune cells, stromal/immune score, immune checkpoints, and sensitivity of chemotherapy drugs were performed in osteosarcoma. Then, a nomogram was built by integrating risk score, age, and gender. Results: A five-hypoxic gene signature was developed for predicting survival outcomes of osteosarcoma patients. ROC curves confirmed that this signature possessed the well predictive performance on osteosarcoma prognosis. Furthermore, it could be independently predictive of prognosis. Metabolism of xenobiotics by cytochrome P450 and nitrogen metabolism were activated in the high-risk samples while cell adhesion molecules cams and intestinal immune network for IgA production were enriched in the low-risk samples. The low-risk samples were characterized by elevated immune cell infiltrations, stromal/immune scores, TNFRSF4 expression, and sensitivity to cisplatin. The nomogram accurately predicted 1-, 3-, and 5-years survival duration. Conclusion: These findings might offer an insight into the optimization of prognosis risk stratification and individualized therapy for osteosarcoma patients.
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Affiliation(s)
- Fengfeng Wu
- Department of Orthopedics and Rehabilitation, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Juntao Xu
- Department of Orthopedics, Huzhou Traditional Chinese Medicine Hospital, Affiliated to Zhejiang Chinese Medical University, Huzhou, China
| | - Mingchao Jin
- Department of Orthopedics, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Xuesheng Jiang
- Department of Orthopedics, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Jianyou Li
- Department of Orthopedics, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Xiongfeng Li
- Department of Orthopedics, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Zhuo Chen
- Department of Orthopedics, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Jiangbo Nie
- Department of Orthopedics, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Zhipeng Meng
- Department of Anesthesiology, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
| | - Guorong Wang
- Department of Orthopedics, Huzhou Central Hospital, Affiliated Central Hospital of Huzhou University, Zhejiang University Huzhou Hospital, Huzhou, China
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40
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Lane B, Khan MT, Choudhury A, Salem A, West CML. Development and validation of a hypoxia-associated signature for lung adenocarcinoma. Sci Rep 2022; 12:1290. [PMID: 35079065 PMCID: PMC8789914 DOI: 10.1038/s41598-022-05385-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
Hypoxia is common in non-small cell lung cancer (NSCLC) and an attractive therapeutic target. As hypoxia-targeting treatments are effective in patients with the most hypoxic tumours, we aimed to develop a lung adenocarcinoma (LUAD) hypoxia-related gene expression signature. RNAseq was used to identify genes significantly differentially expressed under hypoxia (1% O2) in four LUAD cell lines. Identified genes were used for unsupervised clustering of a TCGA-LUAD training dataset (n = 252) and in a machine learning approach to build a hypoxia-related signature. Thirty-five genes were upregulated in common in three of the four lines and reduced in the training cohort to a 28-gene signature. The signature was prognostic in the TCGA training (HR 2.12, 95% CI 1.34-3.37, p = 0.0011) and test (n = 250; HR 2.13, 95% CI 1.32-3.45, p = 0.0016) datasets. The signature was prognostic for overall survival in a meta-analysis of nine other datasets (n = 1257; HR 2.08, 95% CI 1.60-2.70, p < 0.0001). The 28-gene LUAD hypoxia related signature can be taken forward for further validation using a suitable gene expression platform.
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Affiliation(s)
- Brian Lane
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, M20 4BX, UK
| | - Mairah T Khan
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, M20 4BX, UK
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, M20 4BX, UK
| | - Ahmed Salem
- Department Clinical Oncology, Christie NHS Foundation Trust Hospital, Manchester, M204BX, UK
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, M20 4BX, UK.
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41
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O’Connor JD, Overton IM, McMahon SJ. RadSigBench: a framework for benchmarking functional genomics signatures of cancer cell radiosensitivity. Brief Bioinform 2022; 23:6513903. [PMID: 35066588 PMCID: PMC8921666 DOI: 10.1093/bib/bbab561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/20/2022] Open
Abstract
Multiple transcriptomic predictors of tumour cell radiosensitivity (RS) have been proposed, but they have not been benchmarked against one another or to control models. To address this, we present RadSigBench, a comprehensive benchmarking framework for RS signatures. The approach compares candidate models to those developed from randomly resampled control signatures and from cellular processes integral to the radiation response. Robust evaluation of signature accuracy, both overall and for individual tissues, is performed. The NCI60 and Cancer Cell Line Encyclopaedia datasets are integrated into our workflow. Prediction of two measures of RS is assessed: survival fraction after 2 Gy and mean inactivation dose. We apply the RadSigBench framework to seven prominent published signatures of radiation sensitivity and test for equivalence to control signatures. The mean out-of-sample R2 for the published models on test data was very poor at 0.01 (range: −0.05 to 0.09) for Cancer Cell Line Encyclopedia and 0.00 (range: −0.19 to 0.19) in the NCI60 data. The accuracy of both published and cellular process signatures investigated was equivalent to the resampled controls, suggesting that these signatures contain limited radiation-specific information. Enhanced modelling strategies are needed for effective prediction of intrinsic RS to inform clinical treatment regimes. We make recommendations for methodological improvements, for example the inclusion of perturbation data, multiomics, advanced machine learning and mechanistic modelling. Our validation framework provides for robust performance assessment of ongoing developments in intrinsic RS prediction.
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Affiliation(s)
- John D O’Connor
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, BT9 7AE, United Kingdom
| | - Ian M Overton
- Corresponding authors: Ian M. Overton, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972802; E-mail: ; Stephen J. McMahon, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972620; E-mail:
| | - Stephen J McMahon
- Corresponding authors: Ian M. Overton, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972802; E-mail: ; Stephen J. McMahon, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast BT9 7AE, UK. Tel.: +44(0)2890972620; E-mail:
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Cailleteau A, Sargos P, Saad F, Latorzeff I, Supiot S. Drug Intensification in Future Postoperative Radiotherapy Practice in Biochemically-Relapsing Prostate Cancer Patients. Front Oncol 2022; 11:780507. [PMID: 35004302 PMCID: PMC8739777 DOI: 10.3389/fonc.2021.780507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
Although salvage prostate bed radiotherapy is highly effective in biochemically-relapsing prostate cancer patients following prostatectomy, relapses remain frequent and improvements are needed. Randomized phase 3 trials have shown the benefit of adding androgen-depriving therapy to irradiation, but not all patients benefit from this combination. Preclinical studies have shown that novel agents targeting the androgen receptor, DNA repair, PI3K/AKT/mTOR pathways, or the hypoxic microenvironment may help increase the response to prostate bed irradiation while minimizing potential side effects. This perspective review focuses on the most relevant molecules that may have an impact when combined with salvage radiotherapy, and underlines the strategies that need to be developed to increase the efficacy of salvage post-prostatectomy radiotherapy in prostate cancer patients.
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Affiliation(s)
- Axel Cailleteau
- Department of Radiation Oncology, Institut de Cancérologie de l'Ouest, Nantes Saint-Herblain, France
| | - Paul Sargos
- Department of Radiation Oncology, Institut Bergonié, Bordeaux, France
| | - Fred Saad
- Department of Urology, Université de Montréal, Montreal, QC, Canada
| | - Igor Latorzeff
- Department of Radiation Oncology, Oncorad Clinique Pasteur, Toulouse, France
| | - Stéphane Supiot
- Department of Radiation Oncology, Institut de Cancérologie de l'Ouest, Nantes Saint-Herblain, France.,University of Nantes, CRCINA (CNRS, Inserm), Nantes, France
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Lung adenocarcinoma-specific three-integrin signature contributes to poor outcomes by metastasis and immune escape pathways. J Transl Int Med 2021; 9:249-263. [PMID: 35136724 PMCID: PMC8802404 DOI: 10.2478/jtim-2021-0046] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background: Inhibitors targeting integrins (ITGs) are applied as a novel strategy for cancers including lung cancer; however, the heterogeneity of ITG subunits might explain why ITG-targeted inhibitors only show limited efficacy for a small group of lung cancer patients. Materials and methods: RNA-Seq data of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients were obtained from the TCGA database. Cox regression analysis was performed to construct the prognostic signature and generate the nomogram combined with pathologic stages (pStage). GEO datasets were used for verification. The related biological functions were analyzed by Gene Set Enrichment Analysis (GSEA) software and the TIMER database. Results: By Cox regression analysis of 30 ITG subunits, ITG subunit alpha 5 (ITGA5), ITG subunit alpha 6 (ITGA6), and ITG subunit alpha L (ITGAL) were identified as the prognostic factors in LUAD, which were included in the construction of a LUAD-specific 3-ITG signature. Following the calculation of risk score (RS) of each patient based on 3-ITG signature, patients with high RS in LUAD were found to exhibit worse prognosis, especially in early stage. Nomogram combined with RS and pStage could predict the prognosis of LUAD patients accurately. Mechanism exploration by GSEA showed that metastasis-related microenvironmental pathways were significantly enriched in the high-RS group. An elevated expression of ITGA5 was mainly associated with the promotion of cell migration and invasion, while the high expression of ITGAL had a strong positive correlation with the capability of recognizing and killing cancer cells. Conclusions: Three-ITG signature could improve the prediction ability combined with pStage in LUAD and might contribute to poor prognosis by metastasis and immune escape-related pathways.
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Xia H, Wang J, Guo X, Lv Z, Liu J, Yan Q, Liu M, Wang J. Identification of a Hypoxia-Related Gene Signature for Predicting Systemic Metastasis in Prostate Cancer. Front Cell Dev Biol 2021; 9:696364. [PMID: 34722497 PMCID: PMC8548828 DOI: 10.3389/fcell.2021.696364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Systemic metastasis is the main cause of death in patients with prostate cancer. It is necessary to establish a more accurate model to distinguish and predict patients with a high risk of metastasis to optimize individualized treatment. Methods: In this study, it was determined that hypoxia could affect the metastasis-free survival of patients with prostate cancer, and a hypoxia-related gene signature composed of seven genes for predicting metastasis was established and verified in different cohorts. The study further evaluated the effects of ALDOB expression on the proliferation and invasion of the LNCaP and DU145 cell lines under hypoxia and finally constructed a nomogram containing specific clinical characteristics of prostate cancer combined with the hypoxia gene signature to quantify the metastasis risk of individual patients. Results: The hypoxia-related gene signature was identified as an independent risk factor for metastasis-free survival in patients with prostate cancer. The expression of ALDOB increased under hypoxia and promoted the proliferation and invasion of LNCaP and DU145 cells. In addition, patients with a high risk score showed therapeutic resistance and immunosuppression. Compared with other parameters, the nomogram had the strongest predictive power and net clinical benefit. Conclusion: The study established a hypoxia-related gene signature and a nomogram to distinguish and predict patients with a high risk of prostate cancer metastasis, which may help to optimize individualized treatment and explore possible therapeutic targets.
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Affiliation(s)
- Haoran Xia
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianlong Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxiao Guo
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengtong Lv
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingchao Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiuxia Yan
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Fifth School of Clinical Medicine, Peking University, Beijing, China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianye Wang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Xie Z, Cai J, Sun W, Hua S, Wang X, Li A, Jiang J. Development and Validation of Prognostic Model in Transitional Bladder Cancer Based on Inflammatory Response-Associated Genes. Front Oncol 2021; 11:740985. [PMID: 34692520 PMCID: PMC8529162 DOI: 10.3389/fonc.2021.740985] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/16/2021] [Indexed: 01/18/2023] Open
Abstract
Background Bladder cancer is a common malignant type in the world, and over 90% are transitional cell carcinoma. While the impact of inflammatory response on cancer progression has been reported, the role of inflammatory response-associated genes (IRAGs) in transitional bladder cancer still needs to be understood. Methods In this study, IRAGs were download from Molecular Signature Database (MSigDB). The transcriptional expression and matched clinicopathological data were separately obtained from public databases. The TCGA-BLCA cohort was used to identify the differentially expressed IRAGs, and prognostic IRAGs were filtrated by univariate survival analysis. The intersection between them was displayed by Venn diagram. Based on least absolute shrinkage and selection operator (LASSO) regression analysis method, the TCGA-BLCA cohort was used to construct a risk signature. Survival analysis was conducted to calculate the overall survival (OS) in TCGA and GSE13507 cohort between two groups. We then conducted univariate and multivariate survival analyses to identify independently significant indicators for prognosis. Relationships between the risk scores and age, grade, stage, immune cell infiltration, immune function, and drug sensitivity were demonstrated by correlation analysis. The expression level of prognostic genes in vivo and in vitro were determined by qRT-PCR assay. Results Comparing with normal tissues, there were 49 differentially expressed IRAGs in cancer tissues, and 12 of them were markedly related to the prognosis in TCGA cohort for transitional bladder cancer patients. Based on LASSO regression analysis, a risk model consists of 10 IRAGs was established. Comparing with high-risk groups, survival analysis showed that patients in low-risk groups were more likely to have a better survival time in TCGA and GSE13507 cohorts. Besides, the accuracy of the model in predicting prognosis is acceptable, which is demonstrated by receiver operating characteristic curve (ROC) analysis. Age, stage, and risk scores variables were identified as the independently significant indicators for survival in transitional bladder cancer. Correlation analysis represented that the risk score was identified to be significantly related to the above variables except gender variable. Moreover, the expression level of prognostic genes in vivo and in vitro was markedly upregulated for transitional bladder cancer. Conclusions A novel model based on the 10 IRAGs that can be used to predict survival time for transitional bladder cancer. In addition, this study may provide treatment strategies according to the drug sensitivity in the future.
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Affiliation(s)
- Zhiwen Xie
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinming Cai
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenlan Sun
- Department of Geriatrics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Shan Hua
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingjie Wang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Anguo Li
- Department of Urology, The Fifth Peoples Hospital of Zunyi, Guizhou, China
| | - Juntao Jiang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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46
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Xu S, Tang L, Liu Z, Luo C, Cheng Q. Hypoxia-Related lncRNA Correlates With Prognosis and Immune Microenvironment in Lower-Grade Glioma. Front Immunol 2021; 12:731048. [PMID: 34659218 PMCID: PMC8514865 DOI: 10.3389/fimmu.2021.731048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/09/2021] [Indexed: 01/12/2023] Open
Abstract
Background Hypoxia-related genes are demonstrated to correlate with the prognosis of various cancers. However, the role of hypoxia-related long non-coding RNAs (HRLs) in lower-grade glioma (LGG) remains unclear. Methods A total of 700 LGG samples were extracted from TCGA and CGGA databases. Pearson correlation analysis was used to identify HRLs. Lasso analysis was adopted to construct the HRL signature. TIDE algorithm was used to predict responses to immune checkpoint inhibitors. Cell proliferation was estimated by cell counting kit-8 assay, colony formation assay, and EdU assay. Results We identified 340 HRLs and constructed a novel risk signature composed of 19 HRLs. The risk score exhibited potent value in predicting the prognosis of LGG patients and was significantly associated with the prognosis of LGG patients. Moreover, HRL signature could distinguish patients with similar expression levels of immune checkpoints and might predict the efficacy of immune checkpoint inhibitors. Additionally, hypoxia-related pathways and immune pathways were enriched in high-risk group, and high risk score indicated low tumor purity and high immune infiltration. Two major HRLs, LINC00941 and BASP1-AS1, could significantly affect the proliferation of glioma cells. Conclusions Our study constructed a novel HRL signature that could predict the prognosis and immunotherapy response of LGG patients. HRLs could be novel biomarkers to predict the prognosis of LGG patients and potential targets for LGG treatment.
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Affiliation(s)
- Shengchao Xu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Tang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chengke Luo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Wang Z, Fu Y, Xia A, Chen C, Qu J, Xu G, Zou X, Wang Q, Wang S. Prognostic and predictive role of a metabolic rate-limiting enzyme signature in hepatocellular carcinoma. Cell Prolif 2021; 54:e13117. [PMID: 34423480 PMCID: PMC8488553 DOI: 10.1111/cpr.13117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Abnormal expression of metabolic rate-limiting enzymes drives the occurrence and progression of hepatocellular carcinoma (HCC). This study aimed to elucidate the comprehensive model of metabolic rate-limiting enzymes associated with the prognosis of HCC. MATERIALS AND METHODS HCC animal model and TCGA project were used to screen out differentially expressed metabolic rate-limiting enzyme. Cox regression, least absolute shrinkage and selection operation (LASSO) and experimentally verification were performed to identify metabolic rate-limiting enzyme signature. The area under the receiver operating characteristic curve (AUC) and prognostic nomogram were used to assess the efficacy of the signature in the three HCC cohorts (TCGA training cohort, internal cohort and an independent validation cohort). RESULTS A classifier based on three rate-limiting enzymes (RRM1, UCK2 and G6PD) was conducted and serves as independent prognostic factor. This effect was further confirmed in an independent cohort, which indicated that the AUC at year 5 was 0.715 (95% CI: 0.653-0.777) for clinical risk score, whereas it was significantly increased to 0.852 (95% CI: 0.798-0.906) when combination of the clinical with signature risk score. Moreover, a comprehensive nomogram including the signature and clinicopathological aspects resulted in significantly predict the individual outcomes. CONCLUSIONS Our results highlighted the prognostic value of rate-limiting enzymes in HCC, which may be useful for accurate risk assessment in guiding clinical management and treatment decisions.
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Affiliation(s)
- Zhangding Wang
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Yao Fu
- Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Anliang Xia
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Chen Chen
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Jiamu Qu
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Guifang Xu
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaoping Zou
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Qiang Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shouyu Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China.,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Center for Public Health Research, Medical School of Nanjing University, Nanjing, China
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Xu S, Li Z, Hu Y, Zhao W, Jiang J, Feng Z, Chen W, Li C, Chen L, Fang B, Wang H, Zhai Z, Li B, Zeng J, Yang X. Development and validation of a prediction model for axial length elongation in myopic children treated with overnight orthokeratology. Acta Ophthalmol 2021; 99:e686-e693. [PMID: 33191611 DOI: 10.1111/aos.14658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 01/08/2023]
Abstract
PURPOSE To develop and validate a standardized prediction model aiming at 1-year axial length elongation and to guide the orthokeratology lens practice. METHODS This retrospective study was based on medical records of myopic children treated with orthokeratology. Individuals aged 8-15 years (n = 1261) were included and divided into the primary cohort (n = 757) and validation cohort (n = 504). Feature selection was primarily performed to sort out influential predictors by high-throughput extraction. Then, the prediction model was developed using multivariable linear regression analysis completed by backward stepwise selection. Finally, the validation of the prediction model was performed by evaluation metrics (mean-square error, root-mean-square error, mean absolute error and R ad 2 ). RESULTS No significant difference was found between primary and validation cohort (all p > 0.05). After the feature selection, the crude model was adjusted by demographic information in multivariable linear regression analysis, and five final predictors were identified (all p < 0.01). The interaction effect of age with 1-month change of zone-3 mm flat K was detected (p < 0.01); hence, two final prediction models were developed based on two age subgroups. The validation proved an acceptable performance. CONCLUSION An effective multivariable prediction model aiming at 1-year axial length elongation was developed and validated. It can potentially help clinicians to predict orthokeratology efficacy and make valid adjustments. The influential variables revealed in this model can also provide designers directions to optimize the design of lens to improve the efficacy of myopia control.
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Affiliation(s)
- Shengsong Xu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Zhouyue Li
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Yin Hu
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Wenchen Zhao
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Jinyun Jiang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Zhibin Feng
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Weiyin Chen
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Cong Li
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Linxing Chen
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Binglan Fang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Huarong Wang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Zhou Zhai
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Bin Li
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Junwen Zeng
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
| | - Xiao Yang
- State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center Sun Yat‐Sen University Guangzhou China
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Khan MT, Irlam-Jones JJ, Pereira RR, Lane B, Valentine HR, Aragaki K, Dyrskjøt L, McConkey DJ, Hoskin PJ, Choudhury A, West CML. A miRNA signature predicts benefit from addition of hypoxia-modifying therapy to radiation treatment in invasive bladder cancer. Br J Cancer 2021; 125:85-93. [PMID: 33846523 PMCID: PMC8257670 DOI: 10.1038/s41416-021-01326-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND miRNAs are promising biomarkers in oncology as their small size makes them less susceptible to degradation than mRNA in FFPE tissue. We aimed to derive a hypoxia-associated miRNA signature for bladder cancer. METHODS Taqman miRNA array cards identified miRNA seed genes induced under hypoxia in bladder cancer cell lines. A signature was derived using feature selection methods in a TCGA BLCA training data set. miRNA expression data were generated for 190 tumours from the BCON Phase 3 trial and used for independent validation. RESULTS A 14-miRNA hypoxia signature was derived, which was prognostic for poorer overall survival in the TCGA BLCA cohort (n = 403, p = 0.001). Univariable analysis showed that the miRNA signature predicted an overall survival benefit from having carbogen-nicotinamide with radiotherapy (HR = 0.30, 95% CI 0.094-0.95, p = 0.030) and performed similarly to a 24-gene mRNA signature (HR = 0.47, 95% CI 0.24-0.92, p = 0.025). Combining the signatures improved performance (HR = 0.26, 95% CI 0.08-0.82, p = 0.014) with borderline significance for an interaction test (p = 0.065). The interaction test was significant for local relapse-free survival LRFS (p = 0.033). CONCLUSION A 14-miRNA hypoxia signature can be used with an mRNA hypoxia signature to identify bladder cancer patients benefitting most from having carbogen and nicotinamide with radiotherapy.
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Affiliation(s)
- Mairah T. Khan
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Joely J. Irlam-Jones
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Ronnie Rodrigues Pereira
- grid.5379.80000000121662407Translational Oncogenomics, Cancer Research UK Manchester Institute, Oglesby Cancer Research Building, University of Manchester, Manchester, UK
| | - Brian Lane
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Helen R. Valentine
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Kai Aragaki
- grid.21107.350000 0001 2171 9311Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD USA
| | - Lars Dyrskjøt
- grid.154185.c0000 0004 0512 597XDepartment of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - David J. McConkey
- grid.21107.350000 0001 2171 9311Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD USA
| | - Peter J. Hoskin
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Ananya Choudhury
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
| | - Catharine M. L. West
- grid.5379.80000000121662407Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Christie NHS Foundation Trust Hospital, Manchester, UK
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50
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Bibby BAS, Thiruthaneeswaran N, Yang L, Pereira RR, More E, McArt DG, O'Reilly P, Bristow RG, Williams KJ, Choudhury A, West CML. Repurposing FDA approved drugs as radiosensitizers for treating hypoxic prostate cancer. BMC Urol 2021; 21:96. [PMID: 34210300 PMCID: PMC8247203 DOI: 10.1186/s12894-021-00856-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/04/2021] [Indexed: 01/21/2023] Open
Abstract
Background The presence of hypoxia is a poor prognostic factor in prostate cancer and the hypoxic tumor microenvironment promotes radioresistance. There is potential for drug radiotherapy combinations to improve the therapeutic ratio. We aimed to investigate whether hypoxia-associated genes could be used to identify FDA approved drugs for repurposing for the treatment of hypoxic prostate cancer. Methods Hypoxia associated genes were identified and used in the connectivity mapping software QUADrATIC to identify FDA approved drugs as candidates for repurposing. Drugs identified were tested in vitro in prostate cancer cell lines (DU145, PC3, LNCAP). Cytotoxicity was investigated using the sulforhodamine B assay and radiosensitization using a clonogenic assay in normoxia and hypoxia. Results Menadione and gemcitabine had similar cytotoxicity in normoxia and hypoxia in all three cell lines. In DU145 cells, the radiation sensitizer enhancement ratio (SER) of menadione was 1.02 in normoxia and 1.15 in hypoxia. The SER of gemcitabine was 1.27 in normoxia and 1.09 in hypoxia. No radiosensitization was seen in PC3 cells. Conclusion Connectivity mapping can identify FDA approved drugs for potential repurposing that are linked to a radiobiologically relevant phenotype. Gemcitabine and menadione could be further investigated as potential radiosensitizers in prostate cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12894-021-00856-x.
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Affiliation(s)
- Becky A S Bibby
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Niluja Thiruthaneeswaran
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK. .,Sydney Medical School, University of Sydney, Camperdown, Australia.
| | - Lingjian Yang
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Ronnie R Pereira
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK.,Translational Oncogenomics, CRUK Manchester Institute and CRUK Manchester Centre, Manchester, UK
| | - Elisabet More
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Darragh G McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Paul O'Reilly
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Robert G Bristow
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK.,Translational Oncogenomics, CRUK Manchester Institute and CRUK Manchester Centre, Manchester, UK
| | - Kaye J Williams
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, UK
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Science, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
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