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Swahn F, Glavas R, Hultin L, Wickbom M. The advent of the first electric driven EUS-guided 17 gauge core needle biopsy - A pilot study on subepithelial lesions. Scand J Gastroenterol 2024; 59:852-858. [PMID: 38618997 DOI: 10.1080/00365521.2024.2336611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND AND AIMS This pilot study aimed to evaluate safety and tissue sampling from subepithelial lesions (SEL) in the upper gastrointestinal tract with a novel electric motor driven endoscopic ultrasonography (EUS)-guided 17-gauge (G) size core needle biopsy (CNB) instrument. METHODS An investigator-led prospective open label, performance and safety control study, including seven patients (female n = 4, median 71 y, range 28-75) with a determined SEL (median size 30 mm, range 17-150 mm) in the upper digestive tract (stomach n = 6, duodenum n = 1) were eligible and later followed up 14 days after index procedure. All investigations were completed according to protocol with three FNB 22-G passes with four fanning strokes and two EndoDrill® 17-G passes with three fanning strokes. RESULTS Quality of samples as 'visible pieces' (>5 mm): FNB (n = 5/7) (fragmented/blood imbibed n = 1, poor tissue quantity n = 1) compared with 17-G CNB (n = 7/7). Histological result which led to final diagnosis (leiomyoma n = 2, adenocarcinoma n = 1, schwannoma n = 1, neuroendocrine tumour n = 1, desmoid tumour n = 1 and gastrointestinal stromal tumour (GIST) n = 1) could be obtained with the 17-G CNB instrument in all seven patients. FNB technique reached correct diagnosis in six patients. No serious adverse event were recorded. CONCLUSIONS By using an electric driven 17-G biopsy device, a true cylinder of core tissue can be obtained in one single puncture from the area of interest reducing the need for a second sampling. The absolute benefit of EUS-guided CNB is that the sample can be handled and histologically prepared in the same manner as standard percutaneous core needle sample, e.g., breast and prostate cancer.
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Affiliation(s)
- Fredrik Swahn
- Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
- Department of Upper Abdominal Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Robert Glavas
- Department of Surgery, Endoscopy Unit, Linköping University Hospital, Linköping, Sweden
| | - Lucin Hultin
- Department of Pathology and Cytology, Linköping University Hospital, Linköping, Sweden
| | - Malin Wickbom
- Department of Surgery, Örebro University Hospital, Örebro, Sweden
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2
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Zhong Q, Sun R, Aref AT, Noor Z, Anees A, Zhu Y, Lucas N, Poulos RC, Lyu M, Zhu T, Chen GB, Wang Y, Ding X, Rutishauser D, Rupp NJ, Rueschoff JH, Poyet C, Hermanns T, Fankhauser C, Rodríguez Martínez M, Shao W, Buljan M, Neumann JF, Beyer A, Hains PG, Reddel RR, Robinson PJ, Aebersold R, Guo T, Wild PJ. Proteomic-based stratification of intermediate-risk prostate cancer patients. Life Sci Alliance 2024; 7:e202302146. [PMID: 38052461 PMCID: PMC10698198 DOI: 10.26508/lsa.202302146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Gleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in the Gleason grade group (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or overtreatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign sample runs from 278 patients. Three proteins (F5, TMEM126B, and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomize prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management.
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Affiliation(s)
- Qing Zhong
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Rui Sun
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Adel T Aref
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Zainab Noor
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Asim Anees
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Yi Zhu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Natasha Lucas
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Rebecca C Poulos
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Mengge Lyu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tiansheng Zhu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Guo-Bo Chen
- Urology & Nephrology Center, Department of Urology, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yingrui Wang
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xuan Ding
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Jan H Rueschoff
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
| | - Christian Fankhauser
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
- Department of Urology, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | | | - Wenguang Shao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Marija Buljan
- Empa - Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Peter G Hains
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Roger R Reddel
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Phillip J Robinson
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
- Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Tiannan Guo
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Peter J Wild
- Goethe University Frankfurt, Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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3
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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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Lim MH, Shin S, Park K, Park J, Kim SW, Basurrah MA, Lee S, Kim DH. Deep Learning Model for Predicting Airway Organoid Differentiation. Tissue Eng Regen Med 2023; 20:1109-1117. [PMID: 37594633 PMCID: PMC10645934 DOI: 10.1007/s13770-023-00563-8] [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: 11/21/2022] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Organoids are self-organized three-dimensional culture systems and have the advantages of both in vitro and in vivo experiments. However, each organoid has a different degree of self-organization, and methods such as immunofluorescence staining are required for confirmation. Therefore, we established a system to select organoids with high tissue-specific similarity using deep learning without relying on staining by acquiring bright-field images in a non-destructive manner. METHODS We identified four biomarkers in RNA extracted from airway organoids. We also predicted biomarker expression by image-based analysis of organoids by convolution neural network, a deep learning method. RESULTS We predicted airway organoid-specific marker expression from bright-field images of organoids. Organoid differentiation was verified by immunofluorescence staining of the same organoid after predicting biomarker expression in bright-field images. CONCLUSION Our study demonstrates the potential of imaging and deep learning to distinguish organoids with high human tissue similarity in disease research and drug screening.
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Affiliation(s)
- Mi Hyun Lim
- Department of Otolaryngology-Head and Neck Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seocho-gu, Seoul, 06591, Republic of Korea
| | - Seungmin Shin
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 223, 5th Engineering Building 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Keonhyeok Park
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 223, 5th Engineering Building 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Jaejung Park
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 223, 5th Engineering Building 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sung Won Kim
- Department of Otolaryngology-Head and Neck Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seocho-gu, Seoul, 06591, Republic of Korea
| | | | - Seungchul Lee
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 223, 5th Engineering Building 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
- Graduate School of Artificial Intelligence, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
| | - Do Hyun Kim
- Department of Otolaryngology-Head and Neck Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Banpo-daero 222, Seocho-gu, Seoul, 06591, Republic of Korea.
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5
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Röbeck P, Xu L, Ahmed D, Dragomir A, Dahlman P, Häggman M, Ladjevardi S. P-score in preoperative biopsies accurately predicts P-score in final pathology at radical prostatectomy in patients with localized prostate cancer. Prostate 2023; 83:831-839. [PMID: 36938873 DOI: 10.1002/pros.24523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/13/2023] [Accepted: 03/03/2023] [Indexed: 03/21/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is a highly heterogeneous, multifocal disease, and identification of clinically significant lesions is challenging, which complicates the choice of adequate treatment. The Prostatype® score (P-score) is intended to guide treatment decisions for newly diagnosed PCa patients based on a three-gene signature (IGFBP3, F3, and VGLL3) and clinicopathological information obtained at diagnosis. This study evaluated association of the P-score measured in preoperative magnetic resonance imaging/transrectal ultrasound fusion-guided core needle biopsies (CNBs) and the P-score measured in radical prostatectomy (RP) specimens of PCa patients. We also evaluated the P-score association with the pathology of RP specimens. Furthermore, concordance of the P-score in paired CNB and RP specimens, as well as in index versus concomitant nonindex tumor foci from the same RP was investigated. METHODS The study included 100 patients with localized PCa. All patients were diagnosed by CNB and underwent RP between 2015 and 2018. Gene expression was assessed with the Prostatype® real-time quantitative polymerase chain reaction kit and the P-score was calculated. Patients were categorized into three P-score risk groups according to previously defined cutoffs. RESULTS For 71 patients, sufficient CNB tumor material was available for comparison with the RP specimens. The CNB-based P-score was associated with the pathological T-stage in RP specimens (p = 0.02). Moreover, the CNB-based P-score groups were in substantial agreement with the RP-based P-score groups (weighted κ score: 0.76 [95% confidence interval, 95% CI: 0.60-0.92]; Spearman's rank correlation coefficient r = 0.83 [95% CI: 0.74-0.89]; p < 0.0001). Similarly, the P-score groups based on paired index tumor and concomitant nonindex tumor foci (n = 64) were also in substantial agreement (weighted κ score: 0.74 [95% CI: 0.57-0.91]; r = 0.83 [95% CI: 0.73-0.89], p < 0.0001). CONCLUSIONS Our findings suggest that the P-score based on preoperative CNB accurately reflects the pathology of the whole tumor, highlighting its value as a decision support tool for newly diagnosed PCa patients.
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Affiliation(s)
- Pontus Röbeck
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
| | - Lidi Xu
- Prostatype Genomics AB, Stockholm, Sweden
| | | | - Anca Dragomir
- Department of Pathology, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pär Dahlman
- Department of Surgical Sciences, Radiology, Uppsala University Hospital, Uppsala, Sweden
| | - Michael Häggman
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
| | - Sam Ladjevardi
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
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6
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Söderdahl F, Xu LD, Bring J, Häggman M. A Novel Risk Score (P-score) Based on a Three-Gene Signature, for Estimating the Risk of Prostate Cancer-Specific Mortality. Res Rep Urol 2022; 14:203-217. [PMID: 35586706 PMCID: PMC9109804 DOI: 10.2147/rru.s358169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/30/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To develop and validate a risk score (P-score) algorithm which includes previously described three-gene signature and clinicopathological parameters to predict the risk of death from prostate cancer (PCa) in a retrospective cohort. Patients and Methods A total of 591 PCa patients diagnosed between 2003 and 2008 in Stockholm, Sweden, with a median clinical follow-up time of 7.6 years (1–11 years) were included in this study. Expression of a three-gene signature (IGFBP3, F3, VGLL3) was measured in formalin-fixed paraffin-embedded material from diagnostic core needle biopsies (CNB) of these patients. A point-based scoring system based on a Fine-Gray competing risk model was used to establish the P-score based on the three-gene signature combined with PSA value, Gleason score and tumor stage at diagnosis. The endpoint was PCa-specific mortality, while other causes of death were treated as a competing risk. Out of the 591 patients, 315 patients (estimation cohort) were selected to develop the P-score. The P-score was subsequently validated in an independent validation cohort of 276 patients. Results The P-score was established ranging from the integers 0 to 15. Each one-unit increase was associated with a hazard ratio of 1.39 (95% confidence interval: 1.27–1.51, p < 0.001). The P-score was validated and performed better in predicting PCa-specific mortality than both D’Amico (0.76 vs 0.70) and NCCN (0.76 vs 0.71) by using the concordance index for competing risk. Similar improvement patterns are shown by time-dependent area under the curve. As demonstrated by cumulative incidence function, both P-score and gene signature stratified PCa patients into significantly different risk groups. Conclusion We developed the P-score, a risk stratification system for newly diagnosed PCa patients by integrating a three-gene signature measured in CNB tissue. The P-score could provide valuable decision support to distinguish PCa patients with favorable and unfavorable outcomes and hence improve treatment decisions.
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Affiliation(s)
| | - Li-Di Xu
- Prostatype Genomics AB, Stockholm, Sweden
| | | | - Michael Häggman
- Department of Urology, Uppsala University Hospital, Uppsala, Sweden
- Correspondence: Michael Häggman, Department of Urology, Uppsala University Hospital, SE-751 85 Uppsala University Hospital, Uppsala, Sweden, Tel +46 70 520 42 87, Email
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7
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Han Y, Ding Z, Chen B, Liu Y, Liu Y. A Novel Inflammatory Response–Related Gene Signature Improves High-Risk Survival Prediction in Patients With Head and Neck Squamous Cell Carcinoma. Front Genet 2022; 13:767166. [PMID: 35480305 PMCID: PMC9035793 DOI: 10.3389/fgene.2022.767166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/07/2022] [Indexed: 12/21/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a highly prevalent and malignant tumor that is difficult to effectively prognosticate outcomes. Recent reports have suggested that inflammation is strongly related to tumor progression, and several biomarkers linked to inflammation have been demonstrated to be useful for making a prognosis. The goal of this research was to explore the relevance between the inflammatory-related genes and HNSCC prognosis. Methods: The clinical information and gene expression data of patients with HNSCC were acquired from publicly available data sources. A multigene prognostic signature model was constructed in The Cancer Genome Atlas and verified in the Gene Expression Omnibus database. According to the risk score calculated for each patient, they were divided into low- and high-risk groups based on the median. The Kaplan–Meier survival curve and receiver operating characteristic curve were applied to determine the prognostic value of the risk model. Further analysis identified the independent prognostic factors, and a prognostic nomogram was built. The relationship between tumor immune infiltration status and risk scores was investigated using Spearman correlation analysis. Finally, to confirm the expression of genes in HNSCC, quantitative real-time polymerase chain reaction (qRT-PCR) was performed. Results: A prognostic model consisting of 14 inflammatory-related genes was constructed. The samples with a high risk had an apparently shorter overall survival than those with a low risk. Independent prognostic analysis found that risk scores were a separate prognostic factor in HNSCC patients. Immune infiltration analysis suggested that the abundance of B cells, CD8 T cells, M2 macrophages, myeloid dendritic cells, and monocytes in the low-risk group was higher, while that of M0, M1 macrophages, and resting NK cells was obviously higher in the high-risk group. The risk scores were related to chemotherapeutic sensitivity and the expression of several immune checkpoint genes. Moreover, CCL22 and IL10 were significantly higher in HNSCC tissues, as determined by qRT-PCR. Conclusion: Taken together, we constructed a novel inflammatory response–related gene signature, which may be used to estimate outcomes for patients with HNSCC and may be developed into a powerful tool for forecasting the efficacy of immunotherapeutic and chemotherapeutic drugs for HNSCC.
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Affiliation(s)
- Yanxun Han
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Zhao Ding
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Bangjie Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuchen Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Medical University, Hefei, China
- Graduate School of Anhui Medical University, Hefei, China
| | - Yehai Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Yehai Liu,
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Pramana S, Hardiyanta IKY, Hidayat FY, Mariyah S. A comparative assessment on gene expression classification methods of RNA-seq data generated using next-generation sequencing (NGS). NARRA J 2022; 2:e60. [PMID: 38450388 PMCID: PMC10914053 DOI: 10.52225/narra.v2i1.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/22/2022] [Indexed: 03/08/2024]
Abstract
Next-generation sequencing or massively parallel sequencing have revolutionized genomic research. RNA sequencing (RNA-Seq) can profile the gene-expression used for molecular diagnosis, disease classification and providing potential markers of diseases. For classification of gene expressions, several methods that have been proposed are based on microarray data which is a continuous scale or require a normal distribution assumption. As the RNA-Seq data do not meet those requirements, these methods cannot be applied directly. In this study, we compare several classifiers including Logistic Regression, Support Vector Machine, Classification and Regression Trees and Random Forest. A simulation study with different parameters such as over dispersion, differential expression rate is conducted and the results are compared with two mRNA experimental datasets. To measure predictive accuracy six performance indicators are used: Percentage Correctly Classified, Area Under Receiver Operating Characteristic (ROC) Curve, Kolmogorov Smirnov Statistics, Partial Gini Index, H-measure and Brier Score. The result shows that Random Forest outperforms the other classification algorithms.
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Affiliation(s)
| | | | | | - Siti Mariyah
- Politeknik Statistika STIS, Jakarta, Indonesia
- School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
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Quan Y, Zhang X, Ping H. Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation. Cancer Cell Int 2022; 22:33. [PMID: 35045837 PMCID: PMC8772220 DOI: 10.1186/s12935-021-02438-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/30/2021] [Indexed: 02/06/2023] Open
Abstract
Background Epigenetic reprogramming reportedly has a crucial role in prostate cancer (PCa) progression. RNA modification is a hot topic in epigenetics, and N6-methyladenosine (m6A) accounts for approximately 60% of RNA chemical modifications. The aim of this study was to evaluate the m6A modification patterns in PCa patients and construct a risk prediction model using m6A RNA regulators. Materials and methods Analyses were based on the levels of 25 m6A regulators in The Cancer Genome Atlas (TCGA). Differentially expressed gene (DEG) and survival analyses were performed according to TCGA-PRAD clinicopathologic and follow-up information. To detect the influences of m6A regulators and their DEGs, consensus clustering analysis was performed, and tumor mutational burden (TMB) estimation and tumor microenvironment (TME) cell infiltration were assessed. mRNA levels of representative genes were verified using clinical PCa data. Results Diverse expression patterns of m6A regulators between tumor and normal (TN) tissues were detected regarding Gleason score (GS), pathological T stage (pT), TP53 mutation, and survival comparisons, with HNRNPA2B1 and IGFBP3 being intersecting genes. HNRNPA2B1 was upregulated in advanced stages (GS > 7, pT3, HR > 1, and TP53 mutation), as verified using clinical PCa tissue. Three distinct m6A modification patterns were identified through consensus clustering analysis, but no significant difference was found among these groups in recurrence-free survival (RFS) analysis. Six DEGs of m6A clusters (m6Aclusters) were screened through univariate Cox regression analysis. MMAB and PAIAP2 were intersecting genes for the five clinical factors. MMAB, which was upregulated in PCa compared with TN, was verified using clinical PCa samples. Three distinct subgroups were established according to the 6 DEGs. Cluster A involved the most advanced stages and had the poorest RFS. The m6A score (m6Ascore) was calculated based on the 6 genes, and the low m6Ascore group showed poor RFS with a negative association with infiltration for 16 of 23 immune-related cells. Conclusion We screened DEGs of m6Aclusters and identified 6 genes (BAIAP2, TEX264, MMAB, JAGN1, TIMM8AP1, and IMP3), with which we constructed a highly predictive model with prognostic value by dividing TCGA-PRAD into three distinct subgroups and performing m6Ascore analysis. This study helps to elucidate the integral effects of m6A modification patterns on PCa progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02438-1.
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Díez-López C, Tajes Orduña M, Enjuanes Grau C, Moliner Borja P, González-Costello J, García-Romero E, Francesch Manzano J, Yun Viladomat S, Jiménez-Marrero S, Ramos-Polo R, Ras Jiménez MDM, Comín-Colet J. Blood Differential Gene Expression in Patients with Chronic Heart Failure and Systemic Iron Deficiency: Pathways Involved in Pathophysiology and Impact on Clinical Outcomes. J Clin Med 2021; 10:jcm10214937. [PMID: 34768457 PMCID: PMC8585093 DOI: 10.3390/jcm10214937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Iron deficiency is a common disorder in patients with heart failure and is related with adverse outcomes and poor quality of life. Previous experimental studies have shown biological connections between iron homeostasis, mitochondrial metabolism, and myocardial function. However, the mechanisms involved in this crosstalk are yet to be unfolded. Methods: The present research attempts to investigate the intrinsic biological mechanisms between heart failure and iron deficiency and to identify potential prognostic biomarkers by determining the gene expression pattern in the blood of heart failure patients, using whole transcriptome and targeted TaqMan® low-density array analyses. Results: We performed a stepwise cross-sectional longitudinal study in a cohort of chronic heart failure patients with and without systemic iron deficiency. First, the full transcriptome was performed in a nested case-control exploratory cohort of 7 paired patients and underscored 1128 differentially expressed transcripts according to iron status (cohort1#). Later, we analyzed the messenger RNA levels of 22 genes selected by their statistical significance and pathophysiological relevance, in a validation cohort of 71 patients (cohort 2#). Patients with systemic iron deficiency presented lower mRNA levels of mitochondrial ferritin, sirtuin-7, small integral membrane protein 20, adrenomedullin and endothelin converting enzyme-1. An intermediate mitochondrial ferritin gene expression and an intermediate or low sirtuin7 and small integral membrane protein 20 mRNA levels were associated with an increased risk of all-cause mortality and heart failure admission ((HR 2.40, 95% CI 1.04–5.50, p-value = 0.039), (HR 5.49, 95% CI 1.78–16.92, p-value = 0.003), (HR 9.51, 95% CI 2.69–33.53, p-value < 0.001), respectively). Conclusions: Patients with chronic heart failure present different patterns of blood gene expression depending on systemic iron status that affect pivotal genes involved in iron regulation, mitochondrial metabolism, endothelial function and cardiovascular physiology, and correlate with adverse clinical outcomes.
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Affiliation(s)
- Carles Díez-López
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Advanced Heart Failure and Heart Transplant Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
| | - Marta Tajes Orduña
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
| | - Cristina Enjuanes Grau
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Pedro Moliner Borja
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - José González-Costello
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Advanced Heart Failure and Heart Transplant Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
| | - Elena García-Romero
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Advanced Heart Failure and Heart Transplant Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Josep Francesch Manzano
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
| | - Sergi Yun Viladomat
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Internal Medicine, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Santiago Jiménez-Marrero
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Raul Ramos-Polo
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Maria del Mar Ras Jiménez
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Internal Medicine, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Josep Comín-Colet
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Correspondence: ; Tel.: +34-932-607-078
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