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Silagy AW, Sanchez A, Manley BJ, Bensalah K, Bex A, Karam JA, Ljungberg B, Shuch B, Hakimi AA. Harnessing the Genomic Landscape of the Small Renal Mass to Guide Clinical Management. Eur Urol Focus 2019; 5:949-957. [PMID: 31040082 DOI: 10.1016/j.euf.2019.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/30/2019] [Accepted: 04/16/2019] [Indexed: 01/19/2023]
Abstract
CONTEXT Small renal masses (SRMs; tumors <4 cm) encompass a diagnostic and therapeutic challenge. Genomic profiling has the potential to improve risk stratification and personalize treatment selection. OBJECTIVE Herein, we review the evidence regarding the utility, challenges, and potential implications of genomic profiling in the management of SRMs. EVIDENCE ACQUISITION Pertinent publications available on PubMed database pertaining to kidney cancer, tumor size, genomics, and clinical management were reviewed. EVIDENCE SYNTHESIS Compared with larger tumors, SRMs range from benign to lethal, necessitating strategies for improved treatment selection. Recent advances in the molecular characterization of renal cell carcinoma have improved our understanding of the disease; however, utility of these tools for the management of SRMs is less clear. While intratumoral heterogeneity (ITH) reduces the accuracy and reliability of sequencing, relative genomic uniformity of SRMs somewhat lessens the impact of ITH. Therefore, renal mass biopsy of SRMs represents an appealing opportunity to evaluate how incorporation of molecular profiles may improve management strategies. CONCLUSIONS Ongoing research into the genomic landscape of SRMs has advanced our understanding of the spectrum of disease aggressiveness and may hold promise in matching disease biology to treatment intensity. PATIENT SUMMARY Small renal masses are a clinical challenge, as they range from benign to lethal. Genomic profiling may eventually improve treatment selection, but more research is needed.
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Affiliation(s)
- Andrew W Silagy
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Surgery, University of Melbourne, Austin Hospital, Melbourne, Victoria, Australia
| | - Alejandro Sanchez
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brandon J Manley
- Moffitt Cancer Center Genitourinary Oncology and Integrated Mathematical Oncology, Tampa, FL, USA
| | - Karim Bensalah
- Department of Urology, University of Rennes, Rennes, France
| | - Axel Bex
- Royal Free London NHS Foundation Trust and UCL Division of Surgery and Interventional Science, London, UK; The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Brian Shuch
- UCLA School of Medicine, Los Angeles, CA, USA
| | - A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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2
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Banerjee SL, Dionne U, Lambert JP, Bisson N. Targeted proteomics analyses of phosphorylation-dependent signalling networks. J Proteomics 2018; 189:39-47. [DOI: 10.1016/j.jprot.2018.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/19/2018] [Accepted: 02/01/2018] [Indexed: 01/18/2023]
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3
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Di Meo A, Saleeb R, Wala SJ, Khella HW, Ding Q, Zhai H, Krishan K, Krizova A, Gabril M, Evans A, Brimo F, Pasic MD, Finelli A, Diamandis EP, Yousef GM. A miRNA-based classification of renal cell carcinoma subtypes by PCR and in situ hybridization. Oncotarget 2017; 9:2092-2104. [PMID: 29416756 PMCID: PMC5788624 DOI: 10.18632/oncotarget.23162] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/15/2017] [Indexed: 11/25/2022] Open
Abstract
Renal cell carcinoma (RCC) constitutes an array of morphologically and genetically distinct tumors the most prevalent of which are clear cell, papillary, and chromophobe RCC. Accurate distinction between the typically benign-behaving renal oncocytoma and RCC subtypes is a frequent challenge for pathologists. This is critical for clinical decision making. Subtypes also have different survival outcomes and responses to therapy. We extracted RNA from ninety formalin-fixed paraffin-embedded (FFPE) tissues (27 clear cell, 29 papillary, 19 chromophobe, 4 unclassified RCC and 11 oncocytomas). We quantified the expression of six miRNAs (miR-221, miR-222, miR-126, miR-182, miR-200b and miR-200c) by qRT-PCR, and by in situ hybridization in an independent set of tumors. We developed a two-step classifier. In the first step, it uses expression of either miR-221 or miR-222 to distinguish the clear cell and papillary subtypes from chromophobe RCC and oncocytoma (miR-221 AUC: 0.96, 95% CI: 0.9132-1.014, p < 0.0001 and miR-222 AUC: 0.91, 95% CI: 0.8478-0.9772, p < 0.0001). In the second step, it uses miR-126 to discriminate clear cell from papillary RCC (AUC: 1, p < 0.0001) and miR-200b to discriminate chromophobe RCC from oncocytoma (AUC: 0.95, 95% CI: 0.8933-1.021, p < 0.0001). In situ hybridization showed a nuclear staining pattern. miR-126, miR-222 and miR-200b were significantly differentially expressed between the subtypes by in situ hybridization. miRNA expression could distinguish RCC subtypes and oncocytoma. miRNA expression assessed by either PCR or in situ hybridization can be a clinically useful diagnostic tool to complement morphologic renal tumor classification, improving diagnosis and patient management.
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Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rola Saleeb
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Samantha J Wala
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Heba W Khella
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Qiang Ding
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Haiyan Zhai
- BioGenex Laboratories, Fremont, CA, United States of America
| | - Kalra Krishan
- BioGenex Laboratories, Fremont, CA, United States of America
| | - Adriana Krizova
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Manal Gabril
- Department of Pathology, London Health Sciences Center and Western University, London, ON, Canada
| | - Andrew Evans
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Maria D Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, ON, Canada
| | - Antonio Finelli
- Division of Urologic Oncology, Princess Margaret Hospital, University Health Network, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - George M Yousef
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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4
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Delahunt B, Samaratunga H, Martignoni G, Srigley JR, Evans AJ, Brunelli M. Percutaneous renal tumour biopsy. Histopathology 2015; 65:295-308. [PMID: 25041600 DOI: 10.1111/his.12495] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The use of percutaneous renal tumour biopsy (RTB) as a diagnostic tool for the histological characterization of renal masses has increased dramatically within the last 30 years. This increased utilization has paralleled advances in imaging techniques and an evolving knowledge of the clinical value of nephron sparing surgery. Improved biopsy techniques using image guidance, coupled with the use of smaller gauge needles has led to a decrease in complication rates. Reports from series containing a large number of cases have shown the non-diagnostic rate of RTB to range from 4% to 21%. Re-biopsy has been shown to reduce this rate, while the use of molecular markers further improves diagnostic sensitivity. In parallel with refinements of the biopsy procedure, there has been a rapid expansion in our understanding of the complexity of renal cell neoplasia. The 2013 Vancouver Classification is the current classification for renal tumours, and contains five additional entities recognized as novel forms of renal malignancy. The diagnosis of tumour morphotype on RTB is usually achievable on routine histology; however, immunohistochemical studies may be of assistance in difficult cases. The morphology of the main tumour subtypes, based upon the Vancouver Classification, is described and differentiating features are discussed.
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Affiliation(s)
- Brett Delahunt
- Department of Pathology and Molecular Medicine, Wellington School of Medicine and Health Sciences, Wellington, New Zealand
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Austin MC, Smith C, Pritchard CC, Tait JF. DNA Yield From Tissue Samples in Surgical Pathology and Minimum Tissue Requirements for Molecular Testing. Arch Pathol Lab Med 2015; 140:130-3. [DOI: 10.5858/arpa.2015-0082-oa] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context
Complex molecular assays are increasingly used to direct therapy and provide diagnostic and prognostic information but can require relatively large amounts of DNA.
Objectives
To provide data to pathologists to help them assess tissue adequacy and provide prospective guidance on the amount of tissue that should be procured.
Design
We used slide-based measurements to establish a relationship between processed tissue volume and DNA yield by A260 from 366 formalin-fixed, paraffin-embedded tissue samples submitted for the 3 most common molecular assays performed in our laboratory (EGFR, KRAS, and BRAF). We determined the average DNA yield per unit of tissue volume, and we used the distribution of DNA yields to calculate the minimum volume of tissue that should yield sufficient DNA 99% of the time.
Results
All samples with a volume greater than 8 mm3 yielded at least 1 μg of DNA, and more than 80% of samples producing less than 1 μg were extracted from less than 4 mm3 of tissue. Nine square millimeters of tissue should produce more than 1 μg of DNA 99% of the time.
Conclusions
We conclude that 2 tissue cores, each 1 cm long and obtained with an 18-gauge needle, will almost always provide enough DNA for complex multigene assays, and our methodology may be readily extrapolated to individual institutional practice.
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Affiliation(s)
- Melissa C. Austin
- From the Department of Laboratory Medicine, University of Washington Medical Center, Seattle. Dr Austin is now with the Department of Pathology, Walter Reed National Military Medical Center, Bethesda, Maryland
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Jaconi M, Pagni F, Vacirca F, Leni D, Corso R, Cortinovis D, Bidoli P, Bono F, Cuttin MS, Valente MG, Pesci A, Bedini VA, Leone BE. C-arm cone-beam CT-guided transthoracic lung core needle biopsy as a standard diagnostic tool: an observational study. Medicine (Baltimore) 2015; 94:e698. [PMID: 25816042 PMCID: PMC4554007 DOI: 10.1097/md.0000000000000698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
C-arm cone-beam computed tomography (CT)-guided transthoracic lung core needle biopsy (CNB) is a safe and accurate procedure for the evaluation of patients with pulmonary nodules. This article will focus on the clinical features related to CNB in terms of diagnostic performance and complication rate. Moreover, the concept of categorizing pathological diagnosis into 4 categories, which could be used for clinical management, follow-up, and quality assurance is also introduced. We retrospectively collected data regarding 375 C-arm cone-beam CT-guided CNBs from January 2010 and June 2014. Clinical and radiological variables were evaluated in terms of success or failure rate. Pathological reports were inserted in 4 homogenous groups (nondiagnostic--L1, benign--L2, malignant not otherwise specified--L3, and malignant with specific histotype--L4), defining for each category a hierarchy of suggested actions. The sensitivity, specificity, and positive and negative predictive value and accuracy for patients subjected to CNBs were of 96.8%, 100%, 100%, 100%, and 97.2%, respectively. Roughly 75% of our samples were diagnosed as malignant, with 60% lung adenocarcinoma diagnoses. Molecular analyses were performed on 85 malignant samples to verify applicability of targeted therapy. The rate of "nondiagnostic" samples was 12%. C-arm cone-beam CT-guided transthoracic lung CNB can represent the gold standard for the diagnostic evaluation of pulmonary nodules. A clinical and pathological multidisciplinary evaluation of CNBs was needed in terms of integration of radiological, histological, and oncological data. This approach provided exceptional performances in terms of specificity, positive and negative predictive values; sensitivity in our series was lower compared with other large studies, probably due to the application of strong criteria of adequacy for CNBs (L1 class rate). The satisfactory rate of collected material was evaluated not only in terms of merely diagnostic performances but also for predictive results by molecular analysis.
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Affiliation(s)
- Marta Jaconi
- From the Department of Pathology (MJ, FP, FB, MSC, MGV), University Milan Bicocca; Department of Radiology (FV, DL, RC); Department of Oncology (DC, PB); Department of Health Sciences (AP), Pneumology Unit, University Milan Bicocca; Department of Thoracic Surgery (VB), San Gerardo Hospital, Monza; and Department of Pathology (BEL), Desio Hospital, University Milan Bicocca, Desio, Italy
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7
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Carolina de Oliveira Neves A, Fernandes de Araújo Júnior R, Luiza Cabral de Sá Leitão Oliveira A, Antunes de Araújo A, de Lima KMG. The use of EEM fluorescence data and OPLS/UPLS-DA algorithm to discriminate between normal and cancer cell lines: a feasibility study. Analyst 2014; 139:2423-31. [DOI: 10.1039/c4an00296b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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8
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McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov JP, Polley MYC, Kim KY, Tricoli JV, Taylor JMG, Shuman DJ, Simon RM, Doroshow JH, Conley BA. Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration. BMC Med 2013; 11:220. [PMID: 24228635 PMCID: PMC3852338 DOI: 10.1186/1741-7015-11-220] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/06/2013] [Indexed: 12/18/2022] Open
Abstract
High-throughput 'omics' technologies that generate molecular profiles for biospecimens have been extensively used in preclinical studies to reveal molecular subtypes and elucidate the biological mechanisms of disease, and in retrospective studies on clinical specimens to develop mathematical models to predict clinical endpoints. Nevertheless, the translation of these technologies into clinical tests that are useful for guiding management decisions for patients has been relatively slow. It can be difficult to determine when the body of evidence for an omics-based test is sufficiently comprehensive and reliable to support claims that it is ready for clinical use, or even that it is ready for definitive evaluation in a clinical trial in which it may be used to direct patient therapy. Reasons for this difficulty include the exploratory and retrospective nature of many of these studies, the complexity of these assays and their application to clinical specimens, and the many potential pitfalls inherent in the development of mathematical predictor models from the very high-dimensional data generated by these omics technologies. Here we present a checklist of criteria to consider when evaluating the body of evidence supporting the clinical use of a predictor to guide patient therapy. Included are issues pertaining to specimen and assay requirements, the soundness of the process for developing predictor models, expectations regarding clinical study design and conduct, and attention to regulatory, ethical, and legal issues. The proposed checklist should serve as a useful guide to investigators preparing proposals for studies involving the use of omics-based tests. The US National Cancer Institute plans to refer to these guidelines for review of proposals for studies involving omics tests, and it is hoped that other sponsors will adopt the checklist as well.
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Affiliation(s)
- Lisa M McShane
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 5W130, MSC 9735, 9609 Medical Center Drive, Bethesda, MD 20892-9735, USA
| | - Margaret M Cavenagh
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 4W432, MSC 9730, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - Tracy G Lively
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 4W420, MSC 9730, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - David A Eberhard
- Department of Pathology and Lineberger Comprehensive Cancer Center, Brinkhous-Bullitt Bldg., Campus Box 7525, University of North Carolina, Chapel Hill, NC 27599, USA
| | - William L Bigbee
- Department of Pathology and University of Pittsburgh Cancer Institute, Hillman Cancer Center, UPCI Research Pavilion, Suite 2.32b, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - P Mickey Williams
- Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Bldg. 320, Room 2, 1050 Boyles Street, Frederick, MD 21702, USA
| | - Jill P Mesirov
- Computational Biology and Bioinformatics, Broad Institute of Massachusetts Institute of Technology and Harvard University, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Mei-Yin C Polley
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 5W638, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - Kelly Y Kim
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 4W430, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - James V Tricoli
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 3W526, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - Jeremy MG Taylor
- Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA
| | - Deborah J Shuman
- Office of the Director, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 3A44, 31 Center Drive, Bethesda, MD 20892, USA
| | - Richard M Simon
- Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 5W110, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - James H Doroshow
- Office of the Director, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 3A44, 31 Center Drive, Bethesda, MD 20892, USA
| | - Barbara A Conley
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Room 4W426, 9609 Medical Center Drive, Bethesda, MD 20892, USA
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9
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Craven RA, Vasudev NS, Banks RE. Proteomics and the search for biomarkers for renal cancer. Clin Biochem 2013; 46:456-65. [DOI: 10.1016/j.clinbiochem.2012.11.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 12/25/2022]
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