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Buhas BA, Toma V, Beauval JB, Andras I, Couți R, Muntean LAM, Coman RT, Maghiar TA, Știufiuc RI, Lucaciu CM, Crisan N. Label-Free SERS of Urine Components: A Powerful Tool for Discriminating Renal Cell Carcinoma through Multivariate Analysis and Machine Learning Techniques. Int J Mol Sci 2024; 25:3891. [PMID: 38612705 PMCID: PMC11011951 DOI: 10.3390/ijms25073891] [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: 03/02/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The advent of Surface-Enhanced Raman Scattering (SERS) has enabled the exploration and detection of small molecules, particularly in biological fluids such as serum, blood plasma, urine, saliva, and tears. SERS has been proposed as a simple diagnostic technique for various diseases, including cancer. Renal cell carcinoma (RCC) ranks as the sixth most commonly diagnosed cancer in men and is often asymptomatic, with detection occurring incidentally. The onset of symptoms typically aligns with advanced disease, aggressive histology, and unfavorable prognosis, and therefore new methods for an early diagnosis are needed. In this study, we investigated the utility of label-free SERS in urine, coupled with two multivariate analysis approaches: Principal Component Analysis combined with Linear Discriminant Analysis (PCA-LDA) and Support Vector Machine (SVM), to discriminate between 50 RCC patients and 44 healthy donors. Employing LDA-PCA, we achieved a discrimination accuracy of 100% using 13 principal components, and an 88% accuracy in discriminating between different RCC stages. The SVM approach yielded a training accuracy of 100%, a validation accuracy of 99% for discriminating between RCC and controls, and an 80% accuracy for discriminating between stages. The comparative analysis of raw and normalized SERS spectral data shows that while raw data disclose relative concentration variations in urine metabolites between the two classes, the normalization of spectral data significantly improves the accuracy of discrimination. Moreover, the selection of principal components with markedly distinct scores between the two classes serves to alleviate overfitting risks and reduces the number of components employed for discrimination. We obtained the accuracy of the discrimination between the RCC patients cases and healthy donors of 90% for three PCs and a linear discrimination function, and a 88% accuracy of discrimination between stages using six PCs, mitigating practically the risk of overfitting and increasing the robustness of our analysis. Our findings underscore the potential of label-free SERS of urine in conjunction with chemometrics for non-invasive and early RCC detection.
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Affiliation(s)
- Bogdan Adrian Buhas
- Department of Urology, La Croix du Sud Hospital, 52 Chemin de Ribaute St., 31130 Quint Fonsegrives, France; (B.A.B.); (J.-B.B.)
- Department of Urology, Clinical Municipal Hospital, 11 Tabacarilor St., 400139 Cluj-Napoca, Romania; (I.A.); (N.C.)
- Faculty of Medicine and Pharmacy, University of Oradea, 1 Universitatii St., 410087 Oradea, Romania; (R.C.); (T.A.M.)
| | - Valentin Toma
- Department of Nanobiophysics, MedFuture Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 4-6 Pasteur St., 400337 Cluj-Napoca, Romania;
| | - Jean-Baptiste Beauval
- Department of Urology, La Croix du Sud Hospital, 52 Chemin de Ribaute St., 31130 Quint Fonsegrives, France; (B.A.B.); (J.-B.B.)
| | - Iulia Andras
- Department of Urology, Clinical Municipal Hospital, 11 Tabacarilor St., 400139 Cluj-Napoca, Romania; (I.A.); (N.C.)
- Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babes St., 400347 Cluj-Napoca, Romania
| | - Răzvan Couți
- Faculty of Medicine and Pharmacy, University of Oradea, 1 Universitatii St., 410087 Oradea, Romania; (R.C.); (T.A.M.)
| | - Lucia Ana-Maria Muntean
- Department of Medical Education, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babes St., 400347 Cluj-Napoca, Romania;
| | - Radu-Tudor Coman
- Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babes St., 400347 Cluj-Napoca, Romania
| | - Teodor Andrei Maghiar
- Faculty of Medicine and Pharmacy, University of Oradea, 1 Universitatii St., 410087 Oradea, Romania; (R.C.); (T.A.M.)
| | - Rareș-Ionuț Știufiuc
- Department of Nanobiophysics, MedFuture Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 4-6 Pasteur St., 400337 Cluj-Napoca, Romania;
- Department of Pharmaceutical Physics–Biophysics, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 6 Pasteur St., 400349 Cluj-Napoca, Romania
- Nanotechnology Laboratory, TRANSCEND Research Center, Regional Institute of Oncology, 700483 Iași, Romania
| | - Constantin Mihai Lucaciu
- Department of Pharmaceutical Physics–Biophysics, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 6 Pasteur St., 400349 Cluj-Napoca, Romania
| | - Nicolae Crisan
- Department of Urology, Clinical Municipal Hospital, 11 Tabacarilor St., 400139 Cluj-Napoca, Romania; (I.A.); (N.C.)
- Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babes St., 400347 Cluj-Napoca, Romania
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Liu K, Huang Y, Xu Y, Wang G, Cai S, Zhang X, Shi T. BAP1-related signature predicts benefits from immunotherapy over VEGFR/mTOR inhibitors in ccRCC: a retrospective analysis of JAVELIN Renal 101 and checkmate-009/010/025 trials. Cancer Immunol Immunother 2023:10.1007/s00262-023-03424-4. [PMID: 37046008 DOI: 10.1007/s00262-023-03424-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/13/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND In patients with advanced clear cell renal cell carcinoma, despite the undoubted benefits from immune checkpoint inhibitor (ICI)-based therapies over monotherapies of angiogenic/mTOR inhibitors in the intention-to-treat population, approximately a quarter of the patients can scarcely gain advantage from ICIs, prompting the search for predictive biomarkers for patient selection. METHODS Clinical and multi-omic data of 2428 ccRCC patients were obtained from The Cancer Genome Atlas (TCGA, n = 537), JAVELIN Renal 101 (avelumab plus axitinib vs. sunitinib, n = 885), and CheckMate-009/010/025 (nivolumab vs. everolimus, n = 1006). RESULTS BAP1 mutations were associated with large progression-free survival (PFS) benefits from ICI-based immunotherapies over sunitinib/everolimus (pooled estimate of interaction HR = 0.71, 95% CI 0.51-0.99, P = 0.045). Using the top 20 BAP1 mutation-associated differentially expressed genes (DEGs) generated from the TCGA cohort, we developed the BAP1-score, negatively correlated with angiogenesis and positively correlated with multiple immune-related signatures concerning immune cell infiltration, antigen presentation, B/T cell receptor, interleukin, programmed death-1, and interferon. A high BAP1-score indicated remarkable PFS benefits from ICI-based immunotherapies over angiogenic/mTOR inhibitors (avelumab plus axitinib vs. sunitinib: HR = 0.55, 95% CI 0.43-0.70, P < 0.001; nivolumab vs. everolimus: HR = 0.72, 95% CI 0.52-1.00, P = 0.045), while these benefits were negligible in the low BAP1-score subgroup (HR = 1.16 and 1.02, respectively). CONCLUSION In advanced ccRCCs, the BAP1-score is a biologically and clinically significant predictor of immune microenvironment and the clinical benefits from ICI-based immunotherapies over angiogenic/mTOR inhibitors, demonstrating its potential utility in optimizing the personalized therapeutic strategies in patients with advanced ccRCC.
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Affiliation(s)
- Kan Liu
- Department of Urology, The Third Medical Center of PLA General Hospital, Yongding Road 69, Haidian District, Beijing, 100039, China
| | - Yan Huang
- Department of Urology, The Third Medical Center of PLA General Hospital, Yongding Road 69, Haidian District, Beijing, 100039, China
| | - Yu Xu
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | | | - Shangli Cai
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Xu Zhang
- Department of Urology, The Third Medical Center of PLA General Hospital, Yongding Road 69, Haidian District, Beijing, 100039, China.
| | - Taoping Shi
- Department of Urology, The Third Medical Center of PLA General Hospital, Yongding Road 69, Haidian District, Beijing, 100039, China.
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Deciphering intratumor heterogeneity in clear cell renal cell carcinoma utilizing clinicopathologic and molecular platforms. Hum Pathol 2022; 130:95-109. [PMID: 36511267 DOI: 10.1016/j.humpath.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/04/2022]
Abstract
Clear cell renal cell carcinoma (CCRCC) is a common renal malignancy known for its lethality and chromosome 3p aberrancies associated with loss of VHL. It has been shown that additional prognostic molecular markers exist in other transcriptional modifiers such as BAP1 and SETD2. Molecular heterogeneity has been described between primary and metastatic sites as well as genetic diversity in spatial tumor analysis; however, morphologic and proteogenomic heterogeneity information is lacking. We assessed 77 nephrectomy specimens with a diagnosis of CCRCC for morphologic architectural patterns including nodular growth patterns and variations in WHO/ISUP grade. Evaluation of highly heterogeneous areas with immunohistochemical (IHC) staining for BAP1, UCHL1, SETD2, and CAIX was performed and correlated with morphologic and histology data. Ultimately, high variability in the morphologic and histological findings matched the complexity of the IHC findings. Alterations in expression of CAIX and UCHL1 correlated with alterations in transcriptional regulators BAP1 and SETD2 within the tumor. High-grade morphology, such as eosinophilia, were areas enriched for alteration of biomarker expression. This highly complex data set of morphologic and biomarker characteristics highlights the heterogeneity of morphology amongst high-grade CCRCC tumors.
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Webster BR, Gopal N, Ball MW. Tumorigenesis Mechanisms Found in Hereditary Renal Cell Carcinoma: A Review. Genes (Basel) 2022; 13:2122. [PMID: 36421797 PMCID: PMC9690265 DOI: 10.3390/genes13112122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 09/29/2023] Open
Abstract
Renal cell carcinoma is a heterogenous cancer composed of an increasing number of unique subtypes each with their own cellular and tumor behavior. The study of hereditary renal cell carcinoma, which composes just 5% of all types of tumor cases, has allowed for the elucidation of subtype-specific tumorigenesis mechanisms that can also be applied to their sporadic counterparts. This review will focus on the major forms of hereditary renal cell carcinoma and the genetic alterations contributing to their tumorigenesis, including von Hippel Lindau syndrome, Hereditary Papillary Renal Cell Carcinoma, Succinate Dehydrogenase-Deficient Renal Cell Carcinoma, Hereditary Leiomyomatosis and Renal Cell Carcinoma, BRCA Associated Protein 1 Tumor Predisposition Syndrome, Tuberous Sclerosis, Birt-Hogg-Dubé Syndrome and Translocation RCC. The mechanisms for tumorigenesis described in this review are beginning to be exploited via the utilization of novel targets to treat renal cell carcinoma in a subtype-specific fashion.
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Affiliation(s)
| | | | - Mark W. Ball
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute/NIH, 10 Center Drive, CRC Room 2W-5940, Bethesda, MD 20892, USA
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Langbein LE, El Hajjar R, Kim WY, Yang H. The convergence of tumor suppressors on the type I interferon pathway in clear cell renal cell carcinoma and its therapeutic implications. Am J Physiol Cell Physiol 2022; 323:C1417-C1429. [PMID: 36154696 PMCID: PMC9662805 DOI: 10.1152/ajpcell.00255.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/29/2022] [Accepted: 09/17/2022] [Indexed: 01/31/2023]
Abstract
In clear cell renal cell carcinoma (ccRCC), the von Hippel-Lindau tumor suppressor gene/hypoxia inducible factor (VHL/HIF) axis lays the groundwork for tumorigenesis and is the target of many therapeutic agents. HIF activation alone, however, is largely insufficient for kidney tumor development, and secondary mutations in PBRM1, BAP1, SETD2, KDM5C, or other tumor suppressor genes are strong enablers of tumorigenesis. Interestingly, it has been discovered that VHL loss and subsequent HIF activation results in upregulation of a negative feedback loop mediated by ISGF3, a transcription factor activated by type I interferon (IFN). Secondary mutations in the aforementioned tumor suppressor genes all partially disable this negative feedback loop to facilitate tumor growth. The convergence of several cancer genes on this pathway suggests that it plays an important role in ccRCC development and maintenance. Tumors with secondary mutations that dampen the negative feedback loop may be exquisitely sensitive to its reactivation, and pharmacological activation of ISGF3 either alone or in combination with other therapies could be an effective method to treat patients with ccRCC. In this review, we examine the relevance of the type I IFN pathway to ccRCC, synthesize our current knowledge of the ccRCC tumor suppressors in its regulation, and explore how this may impact the future treatment of patients with ccRCC.
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Affiliation(s)
- Lauren E Langbein
- Department of Pathology, Anatomy, & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Rayan El Hajjar
- Department of Pathology, Anatomy, & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - William Y Kim
- Department of Pathology, Anatomy, & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Haifeng Yang
- Department of Pathology, Anatomy, & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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Zhang H, Yin F, Chen M, Yang L, Qi A, Cui W, Yang S, Wen G. Development and Validation of a CT-Based Radiomics Nomogram for Predicting Postoperative Progression-Free Survival in Stage I-III Renal Cell Carcinoma. Front Oncol 2022; 11:742547. [PMID: 35155180 PMCID: PMC8830916 DOI: 10.3389/fonc.2021.742547] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Background Many patients experience recurrence of renal cell carcinoma (RCC) after radical and partial nephrectomy. Radiomics nomogram is a newly used noninvasive tool that could predict tumor phenotypes. Objective To investigate Radiomics Features (RFs) associated with progression-free survival (PFS) of RCC, assessing its incremental value over clinical factors, and to develop a visual nomogram in order to provide reference for individualized treatment. Methods The RFs and clinicopathological data of 175 patients (125 in the training set and 50 in the validation set) with clear cell RCC (ccRCC) were retrospectively analyzed. In the training set, RFs were extracted from multiphase enhanced CT tumor volume and selected using the stability LASSO feature selection algorithm. A radiomics nomogram final model was developed that incorporated the RFs weighted sum and selected clinical predictors based on the multivariate Cox proportional hazard regression. The performances of a clinical variables-only model, RFs-only model, and the final model were compared by receiver operator characteristic (ROC) analysis and DeLong test. Nomogram performance was determined and validated with respect to its discrimination, calibration, reclassification, and clinical usefulness. Results The radiomics nomogram included age, clinical stage, KPS score, and RFs weighted sum, which consisted of 6 selected RFs. The final model showed good discrimination, with a C-index of 0.836 and 0.706 in training and validation, and good calibration. In the training set, the C-index of the final model was significantly larger than the clinical-only model (DeLong test, p = 0.008). From the clinical variables-only model to the final model, the reclassification of net reclassification improvement was 18.03%, and the integrated discrimination improvement was 19.08%. Decision curve analysis demonstrated the clinical usefulness of the radiomics nomogram. Conclusion The CT-based RF is an improvement factor for clinical variables-only model. The radiomics nomogram provides individualized risk assessment of postoperative PFS for patients with RCC.
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Affiliation(s)
- Haijie Zhang
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, China.,PET/CT Center, Department of Nuclear Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Fu Yin
- College of Information Engineering, Shenzhen University, Shenzhen, China
| | - Menglin Chen
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liyang Yang
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Anqi Qi
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weiwei Cui
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shanshan Yang
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ge Wen
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Gallan AJ, Parilla M, Segal J, Ritterhouse L, Antic T. BAP1-Mutated Clear Cell Renal Cell Carcinoma. Am J Clin Pathol 2021; 155:718-728. [PMID: 33210135 DOI: 10.1093/ajcp/aqaa176] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES While aberrations in the VHL gene and chromosome 3p resulting in clear cell renal cell carcinoma (CCRCC) are well established, we know that additional mutations in chromatin remodeling genes PBRM1, SETD2, and BRCA1-associated protein 1 (BAP1) contribute to pathogenesis in some cases. Given the known aggressive clinical behavior of BAP1-mutated CCRCC, we sought to define the pathologic phenotype of BAP1-mutated CCRCC. METHODS We identified 14 cases of molecularly proven BAP1-mutated CCRCC and investigated their clinicopathologic features. RESULTS BAP1-mutated CCRCC frequently showed papillary, tubulopapillary, or expanded nested architecture; demonstrated granular to diffusely eosinophilic cytoplasm with prominent eosinophilic globules; and contained high-grade nuclei. This morphology demonstrates significant overlap with Xp11 translocation renal cell carcinoma (RCC). Immunohistochemistry notably demonstrates loss of BAP1 expression in almost all tumors, in addition to strong p504S expression. A conventional CCRCC component was frequently present adjacent to the characteristic BAP1 areas and showed retained BAP1 expression and only patchy p504S. Approximately two-thirds of BAP1-mutated CCRCCs were stage pT3, renal vein invasion was common, and 50% developed metastases. CONCLUSIONS Herein, we describe the histologic and immunohistochemical findings in BAP1-mutated CCRCC, which has important implications for utilization of molecular testing, prognosis, future therapeutics, and distinction from other RCC subtypes such as Xp11 translocation RCC.
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Affiliation(s)
| | - Megan Parilla
- Department of Pathology, University of Chicago, Chicago, IL
| | - Jeremy Segal
- Department of Pathology, University of Chicago, Chicago, IL
| | | | - Tatjana Antic
- Department of Pathology, University of Chicago, Chicago, IL
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Petitprez F, Ayadi M, de Reyniès A, Fridman WH, Sautès-Fridman C, Job S. Review of Prognostic Expression Markers for Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:643065. [PMID: 33996558 PMCID: PMC8113694 DOI: 10.3389/fonc.2021.643065] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Context: The number of prognostic markers for clear cell renal cell carcinoma (ccRCC) has been increasing regularly over the last 15 years, without being integrated and compared. Objective: Our goal was to perform a review of prognostic markers for ccRCC to lay the ground for their use in the clinics. Evidence Acquisition: PubMed database was searched to identify RNA and protein markers whose expression level was reported as associated with survival of ccRCC patients. Relevant studies were selected through cross-reading by two readers. Evidence Synthesis: We selected 249 studies reporting an association with prognostic of either single markers or multiple-marker models. Altogether, these studies were based on a total of 341 distinct markers and 13 multiple-marker models. Twenty percent of these markers were involved in four biological pathways altered in ccRCC: cell cycle, angiogenesis, hypoxia, and immune response. The main genes (VHL, PBRM1, BAP1, and SETD2) involved in ccRCC carcinogenesis are not the most relevant for assessing survival. Conclusion: Among single markers, the most validated markers were KI67, BIRC5, TP53, CXCR4, and CA9. Of the multiple-marker models, the most famous model, ClearCode34, has been highly validated on several independent datasets, but its clinical utility has not yet been investigated. Patient Summary: Over the years, the prognosis studies have evolved from single markers to multiple-marker models. Our review highlights the highly validated prognostic markers and multiple-marker models and discusses their clinical utility for better therapeutic care.
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Affiliation(s)
- Florent Petitprez
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Mira Ayadi
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Aurélien de Reyniès
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Wolf H. Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Equipe Inflammation, Complément et Cancer, Paris, France
| | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Equipe Inflammation, Complément et Cancer, Paris, France
| | - Sylvie Job
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
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Nuclear up regulation of the BRCA1-associated ubiquitinase BAP1 is associated with tumor aggressiveness in prostate cancers lacking the TMPRSS2:ERG fusion. Oncotarget 2019; 10:7096-7111. [PMID: 31903168 PMCID: PMC6935259 DOI: 10.18632/oncotarget.27270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/24/2019] [Indexed: 01/21/2023] Open
Abstract
Loss of the putative tumor suppressor BAP1 is a candidate biomarker for adverse prognosis in many cancer types, but conversely for improved survival in others. Studies on the expression and prognostic role of BAP1 in prostate cancer are currently lacking. We used a tissue microarray of 17,747 individual prostate cancer samples linked with comprehensive pathological, clinical and molecular data and studied the immunohistochemical expression of BAP1. BAP1 expression was typically up regulated in cancers as compared to adjacent normal prostatic glands. In 15,857 cancers, BAP1 staining was weak in 3.3%, moderate in 41.6% and strong in 17.4%. Strong BAP1 staining was associated with advanced tumor stage (p<0.0001), high classical and quantitative Gleason grade (p<0.0001), lymph node metastasis (p<0.0001), a positive surgical margin (p=0.0019) and early biochemical recurrence (p<0.0001). BAP1 expression was linked to ERG-fusion type cancers, with strong BAP1 staining in 12% of ERG-negative, but 30% of ERG-positive cancers (p<0.0001). Subset analyses in 5,415 cancers with and 4,217 cancers without TMPRSS2:ERG fusion revealed that these associations with tumor phenotype and patient outcome were largely driven by the subset of ERG-negative tumors. Multivariate analysis revealed that the prognostic impact was independent of established prognostic features in ERG negative p<0.001) but not in ERG positive cancers. BAP1 expression was further linked to androgen receptor (AR) expression: Only 2% of AR-negative, but 33% of strongly AR expressing cancers had strong BAP1 expression (p<0.0001). In conclusion, this study shows that BAP1 up regulation is linked to prostate cancer progression and aggressiveness.
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Kakkar A, Guleria P, Madan K, Kumar R, Kumar S, Jain D. Immunohistochemical Assessment of BAP1 Protein in Mucoepidermoid Carcinomas. Indian J Otolaryngol Head Neck Surg 2019; 71:33-37. [PMID: 30906710 DOI: 10.1007/s12070-018-1549-3] [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: 10/07/2018] [Accepted: 12/04/2018] [Indexed: 11/29/2022] Open
Abstract
Mucoepidermoid carcinomas are common malignant salivary gland tumors. Despite recent advances in diagnosis and treatment, there has not been much improvement in outcome of these patients, necessitating identification of novel targeted therapeutic agents. Genomic profiling of mucoepidermoid carcinomas has recently revealed aberrations in BAP1 gene. Therefore, we conducted this study to identify BAP1 loss by immunohistochemistry in these tumors. Mucoepidermoid carcinoma cases were retrieved; hematoxylin-and-eosin stained sections were reviewed. Immunohistochemistry for BAP1 was performed. Forty cases were assessed, including 25 salivary gland and 15 pulmonary mucoepidermoid carcinomas. There were 19 cases in the parotid (76%), two in submandibular gland (8%), and remaining 16% from minor salivary gland locations. Ten (40%) were low grade, nine (36%) were intermediate grade, and six (24%) were high grade mucoepidermoid carcinomas. Thirteen (86.7%) pulmonary mucoepidermoid carcinomas were tracheobronchial, while two (13.3%) were intraparenchymal; all were low grade mucoepidermoid carcinomas. On immunohistochemistry, BAP1 nuclear staining was retained in all cases (100%), irrespective of tumor location or grade. Therapeutic connotations necessitate the identification of readily applicable techniques to detect BAP1 loss in mucoepidermoid carcinomas. Using immunohistochemistry, loss of BAP1 staining was not seen in any of our cases, suggesting insensitivity of BAP1 IHC to detect aberrations at genomic level in these tumors. Analysis of BAP1 alterations by targeted sequencing may therefore be performed prior to excluding the possibility of response to BAP1-targeted therapeutics based on immunohistochemistry alone.
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Affiliation(s)
- Aanchal Kakkar
- 1Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Prerna Guleria
- 1Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Karan Madan
- 2Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Rajeev Kumar
- 3Department of Otorhinolaryngology and Head and Neck Surgery, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Sunil Kumar
- 4Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, 110029 India
| | - Deepali Jain
- 1Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029 India
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Bihr S, Ohashi R, Moore AL, Rüschoff JH, Beisel C, Hermanns T, Mischo A, Corrò C, Beyer J, Beerenwinkel N, Moch H, Schraml P. Expression and Mutation Patterns of PBRM1, BAP1 and SETD2 Mirror Specific Evolutionary Subtypes in Clear Cell Renal Cell Carcinoma. Neoplasia 2019; 21:247-256. [PMID: 30660076 PMCID: PMC6355619 DOI: 10.1016/j.neo.2018.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/14/2018] [Accepted: 12/22/2018] [Indexed: 12/16/2022] Open
Abstract
Bi-allelic inactivation of the VHL gene on chromosome 3p is the characteristic feature in most clear cell renal cell carcinomas (ccRCC). Frequent gene alterations were also identified in SETD2, BAP1 and PBRM1, all of which are situated on chromosome 3p and encode histone/chromatin regulators. The relationship between gene mutation, loss of protein expression and the correlations with clinicopathological parameters is important for the understanding of renal cancer progression. We analyzed PBRM1 and BAP1 protein expression as well as the tri-methylation state of H3K36 as a surrogate marker for SETD2 activity in more than 700 RCC samples. In ccRCC loss of nuclear PBRM1 (68%), BAP1 (40%) and H3K36me3 (47%) expression was significantly correlated with each other, advanced tumor stage, poor tumor differentiation (P < .0001 each), and necrosis (P < .005) Targeted next generation sequencing of 83 ccRCC samples demonstrated a significant association of genetic mutations in PBRM1, BAP1, and SETD2 with absence of PBRM1, BAP1, and HEK36me3 protein expression (P < .05, each). By assigning the protein expression patterns to evolutionary subtypes, we revealed similar clinical phenotypes as suggested by TRACERx Renal. Given their important contribution to tumor suppression, we conclude that combined functional inactivation of PBRM1, BAP1, SETD2 and pVHL is critical for ccRCC progression.
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Affiliation(s)
- Svenja Bihr
- Department of Oncology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Riuko Ohashi
- Histopathology Core Facility, Niigata University Faculty of Medicine, Niigata, Japan
| | - Ariane L Moore
- Department of Biosystems Science and Engineering, ETH, Zurich, Basel, Switzerland
| | - Jan H Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH, Zurich, Basel, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Axel Mischo
- Department of Oncology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Claudia Corrò
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Jörg Beyer
- Department of Oncology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH, Zurich, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland.
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12
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Wu J, Wang H, Ricketts CJ, Yang Y, Merino MJ, Zhang H, Shi G, Gan H, Linehan WM, Zhu Y, Ye D. Germline mutations of renal cancer predisposition genes and clinical relevance in Chinese patients with sporadic, early-onset disease. Cancer 2018; 125:1060-1069. [PMID: 30548481 DOI: 10.1002/cncr.31908] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/04/2018] [Accepted: 11/12/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND An inherited susceptibility to renal cancers is associated with multiple predisposing genes, but most screening tests are limited to patients with a family history. Next-generation sequencing (NGS)-based multigene panels provide an efficient and adaptable tool for investigating pathogenic germline mutations on a larger scale. This study investigated the frequency of pathogenic germline mutations in renal cancer predisposition genes in patients with sporadic, early-onset disease. METHODS An NGS-based panel of 23 known and potential renal cancer predisposition genes was used to analyze germline mutations in 190 unrelated Chinese patients under the age of 45 years who presented with renal tumors. The detected variants were filtered for pathogenicity, and then their frequencies were calculated and correlated with clinical features. Germline variants of the fumarate hydratase (FH) and BRCA1-associated protein 1 (BAP1) genes were comprehensively analyzed because of their aggressive potential. RESULTS In total, 18 patients (9.5%) had germline mutations in 10 genes. Twelve of these 18 patients had alterations in renal cancer predisposition genes (6.3%), and 6 patients had mutations in potential predisposition genes such as BRCA1/2. Notably, pathogenic mutation carriers had a significant family history in second-degree relatives in comparison with those without pathogenic mutations (P < .001). Variants of unknown clinical significance in FH and BAP1 demonstrated evidence of additional somatic loss in tumors. CONCLUSIONS In patients with early-onset disease, a multigene panel identified a high pathogenic germline mutation rate in renal cancer predisposition genes. This study emphasizes the importance of screening patients with early-onset disease for mutations in cancer predisposition genes. Germline screening should be encouraged in early-onset patients to provide personalized medicine and improve patient outcomes.
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Affiliation(s)
- Junlong Wu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Hongkai Wang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maria J Merino
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Hualei Gan
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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13
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Loss of BAP1 expression in metastatic tumor tissue is an event of poor prognosis in patients with metastatic clear cell renal cell carcinoma. Urol Oncol 2018; 37:78-85. [PMID: 30446457 DOI: 10.1016/j.urolonc.2018.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/08/2018] [Accepted: 10/13/2018] [Indexed: 11/23/2022]
Abstract
PURPOSE To evaluate the prognostic impact of the protein expression of both PBRM1 and BAP1 in metastatic tissue of patients with metastatic clear cell renal cell carcinoma (ccRCC). PATIENTS AND METHODS In all 124 consecutive cases of metastatic ccRCC, who underwent metastasectomy or biopsy of metastatic tumor tissue between 2007 and 2016 were selected from the medical records of our institution. Additionally, 38 paired cases with tissue from the primary tumor involving radical or partial nephrectomy for ccRCC were also selected. All cases were reviewed for uniform reclassification and the most representative tumor areas were selected for the construction of a tissue microarray. RESULTS PBRM1 nuclear staining of the 124-immunostained metastases of ccRCC specimens showed that 98 (79.0%) had negative expression and 26 (21.0%) positive expression of PBRM1. Regarding BAP1 expression, we observed that 77 (62.1%) specimens were negative and 47 (37.9%) showed positive nuclear staining. When we compared the expression of both markers on primary tumor and tumor metastasis, we found disagreement in half of the cases. Five-year overall survival rates in patients with positive expression and negative expression of BAP1 were 53.2% and 35.1%, respectively (P = 0.004). Five-year progression-free survival rates in patients with positive expression and negative expression of BAP1 were 14.9% and 3.9%, respectively (P = 0.003). Conversely, PBRM1 expression did not significantly influence either overall survival or progression-free survival rates. In multivariate analysis, negative expression of BAP1 tumors also presented higher risks of death (hazard ratio (HR) = 1.913, P = 0.041) and disease progression (HR = 1.656, P = 0.021). CONCLUSION The use of prognostic biomarkers identified in the primary tumor tissue might be not reliable in the metastatic disease scenario. Patients with metastatic ccRCC that present loss of BAP1 expression in metastatic tissue demonstrated poor survival rates and represent a relevant risk group for tumor recurrence and death.
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14
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Jin S, Wu J, Zhu Y, Gu W, Wan F, Xiao W, Dai B, Zhang H, Shi G, Shen Y, Zhu Y, Ye D. Comprehensive Analysis of BAP1 Somatic Mutation in Clear Cell Renal Cell Carcinoma to Explore Potential Mechanisms in Silico. J Cancer 2018; 9:4108-4116. [PMID: 30519310 PMCID: PMC6277624 DOI: 10.7150/jca.27281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/24/2018] [Indexed: 12/29/2022] Open
Abstract
Purpose: Aim of this study was to comprehensively analyze BRCA1-associated protein-1 (BAP1) somatic mutation in clear cell renal cell carcinoma (ccRCC) and explore potential therapeutic pathways and molecules. Patients and methods: In this study, we analyzed 445 ccRCC cases from The Cancer Genome Atlas (TCGA). Comprehensive analysis including survival, transcriptome and methylation between BAP1 mutated and wild-type cases was performed using bioinformatics tools in silico. Pathways and molecules related to BAP1 mutation were analyzed using Database for Annotation, Visualization and Integrated Discovery (DAVID) and protein-protein interaction (PPI) network. Results: BAP1 mutated ccRCC patients had a worse overall survival (OS) and disease free survival (DFS) than BAP1 wild-type patients. We found 583 up-regulated and 1216 down-regulated different expressed genes (DEGs) in BAP1 mutated tumors. Up-regulated DEGs were enriched in molecular functions and biological processes like protein binding, protein transport and ubiquitin protein ligase binding. Down-regulated DEGs were enriched in pathways like Rap1 signaling pathway, Notch pathway and altered molecular functions like metal ion binding and ubiquitin-protein transferase activity. Furthermore, CAD, TSPO, CTNNB1 and MAPK3 were top hub genes selected using PPI network analysis. Finally, BAP1 mutation had a strong correlation with CpG island methylator phenotype (CIMP). Conclusion: Our study provides a comprehensive understanding of BAP1 functional somatic mutation in ccRCC patients. Several hub genes like CAD and TSPO may become potential therapeutic targets.
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Affiliation(s)
- Shengming Jin
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Junlong Wu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weijie Gu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjun Xiao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yijun Shen
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiping Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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15
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Abstract
PURPOSE OF REVIEW Large-scale genomic profiling has shed new light on the molecular underpinnings of renal cell carcinoma (RCC), spurring a much needed refinement of RCC subclassification based on an integrative assessment of histopathologic features and molecular alterations. At the same time, renal mass biopsies have become increasingly commonplace, necessitating ancillary tools to help guide clinical management. Herein, we briefly review our current understanding of RCC genomics, highlighting areas of possible clinical utility, as well as potential limitations, for renal mass biopsies. RECENT FINDINGS Distinct RCC subtypes harbor characteristic molecular features, including somatic mutations, copy number alterations, and genomic rearrangements. Existing ancillary tools, including fluorescent in-situ hybridization and immunohistochemistry, may be useful for diagnostic subclassification. Recurrent secondary molecular alterations in clear cell RCC (BAP1, SETD2, PBRM1, and TP53) and papillary RCC (CDKN2A) may be associated with poor prognosis; however, intratumoral genomic heterogeneity may limit the clinical utility of these molecular biomarkers in renal mass biopsies. SUMMARY Recent technological advances have the potential to fundamentally alter the clinical management of RCC by leveraging our increasing understanding of RCC genomics to assess hundreds of molecular biomarkers simultaneously. Additional focused molecular analyses of renal mass biopsy cohorts are needed prior to widespread implementation of molecular biomarker assays.
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16
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Abstract
Renal cell carcinoma (RCC) is a heterogenous group of tumors, >70% of which belong to the category of clear cell carcinoma. In recent years, crucial advances have been made in our understanding of the molecular and metabolic basis of clear cell carcinoma. This tumor manifests significant alterations in the cellular metabolism, so that the tumor cells preferentially induce the hypoxia response pathway using aerobic glycolysis, rather than the normal oxidative phosphorylation for energy. Most of the clear cell carcinomas (sporadic as well as familial) have mutations and deletions in the VHL gene located at 3p (p3.25). Normally, pVHL plays a crucial role in the proteasomal degradation of hypoxia-inducible factors (HIF)1 and HIF2. Lack of a functioning pVHL owing to genetic alterations results in stabilization and accumulation of these factors, which promotes cell growth, cell proliferation, and angiogenesis, contributing to a neoplastic phenotype. Several other genes normally located adjacent to VHL (BAP1, SETD2, PBRM1) may also be lost. These are tumor suppressor genes whose loss not only plays a role in carcinogenesis but may also influence the clinical course of these neoplasms. In addition, interaction among a variety of other genes located at several different chromosomes may also play a role in the genesis and progression of clear cell carcinoma.
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17
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da Costa WH, da Cunha IW, Fares AF, Bezerra SM, Shultz L, Clavijo DA, da Silva DV, Netto GJ, Guimaraes GC, Cassio Zequi SD. Prognostic impact of concomitant loss of PBRM1 and BAP1 protein expression in early stages of clear cell renal cell carcinoma. Urol Oncol 2018; 36:243.e1-243.e8. [DOI: 10.1016/j.urolonc.2018.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/04/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
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18
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Wang Z, Wang XY, Li J, Zhu WW. Prognostic and Clinicopathological Significance of BAP1 Protein Expression in Different Types of Cancer—A Meta-Analysis. Genet Test Mol Biomarkers 2018; 22:115-126. [PMID: 29266978 DOI: 10.1089/gtmb.2017.0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Zheng Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
| | - Xiang-Yu Wang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
| | - Juan Li
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
| | - Wen-Wei Zhu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institutes of Cancer Metastasis, Fudan University, Shanghai, China
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19
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Minardi D, Lucarini G, Milanese G, Montironi R, Di Primio R. Prognostic role of BAP1 in pT1 clear cell carcinoma in partial nephrectomy specimens. Virchows Arch 2017; 471:99-105. [PMID: 28488170 DOI: 10.1007/s00428-017-2143-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 12/21/2022]
Abstract
BAP1 is a gene situated on chromosome 3p in a region that can be modified in renal cell carcinomas (RCCs). Mutations that cause loss of expression of BAP1 frequently occur in primary clear cell renal carcinoma (ccRCC). In a previous work, we observed that loss of nuclear BAP1 expression was crucial in ccRCC progression; in the current study, we investigated BAP1 expression in a large series of small conventional ccRCCs treated with partial nephrectomy, to assess a possible role as biomarker and the prognostic value in terms of patients' survival at long-term follow-up. One hundred sixty-two patients with single pT1 ccRCC were selected from those who underwent surgery at our Institute of Urology between 1987 and 2000. The features considered in this study were gender, age, tumor size, grade, incidence of metastasis, and patient-specific survival; they were correlated with immunohistochemical BAP1 nuclear expression in tumoral tissue. Median follow-up was 197.24 months (range 19 to 274); median survival was 125.34 months (range 5 to 274 months). None of our pT1 ccRCCs showed total loss of nuclear BAP1 staining; we found a significant negative correlation between nuclear BAP1 expression and tumor size and between nuclear BAP1 expression and grade. In small ccRCCs, nuclear BAP1 staining was not correlated with disease-specific 5-year survival.Our data confirm the established role of BAP1 as a tumor suppressor protein. This is the first report where BAP1 has been studied in pT1 ccRCC tumors, but nuclear BAP1 expression cannot help identify patients having high-risk disease in these patients.
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Affiliation(s)
- Daniele Minardi
- Dipartimento di Scienze Cliniche e Specialistiche - Sezione di Urologia, Università Politecnica delle Marche - Azienda Ospedaliero-Universitaria Ospedali Riuniti, via Conca, 71, Ancona, Italy.
| | - Guendalina Lucarini
- Dipartimento di Scienze Cliniche e Molecolari - Sezione di Istologia, Università Politecnica delle Marche, Ancona, Italy
| | - Giulio Milanese
- Dipartimento di Scienze Cliniche e Specialistiche - Sezione di Urologia, Università Politecnica delle Marche - Azienda Ospedaliero-Universitaria Ospedali Riuniti, via Conca, 71, Ancona, Italy
| | - Rodolfo Montironi
- Dipartimento di Scienze Biomediche e Sanità Pubblica - Sezione di Patologia e Istopatologia, Università Politecnica delle Marche - Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Roberto Di Primio
- Dipartimento di Scienze Cliniche e Molecolari - Sezione di Istologia, Università Politecnica delle Marche, Ancona, Italy
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20
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Leblay N, Leprêtre F, Le Stang N, Gautier-Stein A, Villeneuve L, Isaac S, Maillet D, Galateau-Sallé F, Villenet C, Sebda S, Goracci A, Byrnes G, McKay JD, Figeac M, Glehen O, Gilly FN, Foll M, Fernandez-Cuesta L, Brevet M. BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas. J Thorac Oncol 2017; 12:724-733. [PMID: 28034829 DOI: 10.1016/j.jtho.2016.12.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Malignant mesothelioma is a deadly disease that is strongly associated with asbestos exposure. Peritoneal mesotheliomas account for 10% of all the cases. BRCA1 associated protein 1 (BAP1) is a deubiquitinating hydrolase that plays a key role in various cellular processes. Germline and somatic inactivation of BRCA1 associated protein 1 gene (BAP1) is frequent in pleural mesothelioma; however, little is known about its status in peritoneal mesothelioma. METHODS Taking advantage of the extensive French National Network for the Diagnosis of Malignant Pleural Mesothelioma and Rare Peritoneal Tumors and the French National Network for the Treatment of Rare Peritoneal Surface Malignancies, we collected biological material and clinical and epidemiological data for 46 patients with peritoneal mesothelioma. The status of BAP1 was evaluated at the mutational and protein expression levels and combined with our previous data on copy number alterations assessed in the same samples. RESULTS We detected mutations in 32% of the malignant peritoneal mesotheliomas analyzed. In addition, we have previously reported that copy number losses occurred in 42% of the samples included in this series. Overall, 73% of the malignant peritoneal mesotheliomas analyzed carried at least one inactivated BAP1 allele, but only 57% had a complete loss of its protein nuclear expression. Better overall survival was observed for patients with BAP1 mutations (p = 0.04), protein expression loss (p = 0.016), or at least one of these alterations (p = 0.007) independently of tumor histological subtype, age, and sex. CONCLUSIONS As in pleural mesothelioma, inactivation of BAP1 is frequent in peritoneal mesotheliomas. We found that BAP1 protein nuclear expression is a good prognostic factor and a more reliable marker for the complete loss of BAP1 activity than mutation or copy number loss.
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Affiliation(s)
- Noémie Leblay
- International Agency for Research on Cancer, Lyon, France
| | - Frédéric Leprêtre
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France
| | - Nolwenn Le Stang
- Department of Biopathology, Cancer Center Lyon Leon Berard, Lyon, France; National Cancer Institute, Research Unit 1086, Caen, France
| | | | - Laurent Villeneuve
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; University Hospital of Lyon, Lyon, France
| | - Sylvie Isaac
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Pathology, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Denis Maillet
- Department of Oncology, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Françoise Galateau-Sallé
- Department of Biopathology, Cancer Center Lyon Leon Berard, Lyon, France; National Cancer Institute, Research Unit 1086, Caen, France
| | - Céline Villenet
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France
| | - Shéhérazade Sebda
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France
| | - Alexandra Goracci
- Department of Radiology, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Graham Byrnes
- International Agency for Research on Cancer, Lyon, France
| | - James D McKay
- International Agency for Research on Cancer, Lyon, France
| | - Martin Figeac
- Structural and Functional Genomics Core Facility, University of Lille, Lille, France; Sequencing Platform, Research Cancer Institute, Lille, France
| | - Olivier Glehen
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Surgery, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - François-Noël Gilly
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Surgery, University Hospital of Lyon and Lyon1 University, Lyon, France
| | - Matthieu Foll
- International Agency for Research on Cancer, Lyon, France
| | | | - Marie Brevet
- Faculty of Medicine, Research Team 3738, Lyon1 University, Oullins, France; French National Network for the Treatment of Rare Peritoneal Surface Malignancies, University Hospital of Lyon and Lyon1 University, Lyon, France; Department of Pathology, University Hospital of Lyon and Lyon1 University, Lyon, France
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Xi J, Feng J, Li Q, Li X, Zeng S. The long non-coding RNA lncFOXO1 suppresses growth of human breast cancer cells through association with BAP1. Int J Oncol 2017; 50:1663-1670. [PMID: 28339037 DOI: 10.3892/ijo.2017.3933] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 11/06/2022] Open
Abstract
Breast cancer, one of the common cancers of women, is the leading cause of death among women below the age of 50 years in western countries. Long non-coding RNAs (lncRNAs) have been shown to be involved in diverse biological processes, both physical and pathological. However, to date, only a few lncRNAs have been functionally identified in breast cancer, and the overall pathophysiological contributions of lncRNAs to breast cancer remain largely unknown. In the present study, we identified a novel lncRNA termed lncFOXO1 through microarray screening. lncFOXO1 is significantly decreased in breast cancer tissues and cell lines and downregulation of lncFOXO1 expression associates with poorer overall survival. Functional assays demonstrated its suppressive role in breast cancer in vivo and in vitro. Mechanistically, lncFOXO1 suppressed the growth of breast cancer by increasing FOXO1 transcription. Moreover, we found that lncFOXO1 associated with BRCA-1-associated protein 1 (BAP1) and regulates its binding and the level of mono-ubiquitinated H2A at K119 (ubH2AK119) at FOXO1 promoter.
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Affiliation(s)
- Jie Xi
- Department of Gynecology, Cangzhou Central Hospital, Cangzhou, Heibei 061001, P.R. China
| | - Jing Feng
- Department of Gynecology, Cangzhou Central Hospital, Cangzhou, Heibei 061001, P.R. China
| | - Qian Li
- Department of Gynecology, Cangzhou Central Hospital, Cangzhou, Heibei 061001, P.R. China
| | - Xia Li
- Department of Gynecology, Cangzhou Central Hospital, Cangzhou, Heibei 061001, P.R. China
| | - Saitian Zeng
- Department of Gynecology, Cangzhou Central Hospital, Cangzhou, Heibei 061001, P.R. China
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22
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Itoh J, Ito A, Shimada S, Kawasaki Y, Kakoi N, Saito H, Mitsuzuka K, Watanabe M, Satoh M, Saito S, Arai Y. Clinicopathological significance of ganglioside DSGb5 expression in renal cell carcinoma. Glycoconj J 2017; 34:267-273. [PMID: 28205070 DOI: 10.1007/s10719-017-9763-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/31/2017] [Accepted: 02/07/2017] [Indexed: 11/26/2022]
Abstract
Disialosyl globopentaosylceramide (DSGb5) is a ganglioside originally isolated from tissue extracts of renal cell carcinoma (RCC) with metastasis. Previous in vitro experiments have suggested that DSGb5 promotes metastasis by enhancing the migration of RCC cells and downregulating NK cell cytotoxicity against RCC cells. In this study, we investigated the clinicopathological significance of DSGb5 expression in RCC and outcomes of RCC patients. A total of 156 RCC patients who underwent surgical treatments at our hospital from January 2007 through December 2012 were analyzed in this study. The expression of DSGb5 in RCC specimens was examined by immunohistochemical staining with monoclonal antibody 5F3. The immunostaining intensity of RCC tissues was assessed in comparison with that in benign renal tubules as an internal positive control. The relationship between DSGb5 expression and clinicopathological characteristics was investigated and recurrence free survival following surgery was evaluated. Microvascular invasion was observed in 68% (n = 19/28) and in 45% (n = 58/128) of the DSGb5 high expression group and low expression group, respectively (p = 0.031). Of 156 patients with a median follow up of 51 months, 18 patients (12%) developed metastasis following surgery. Patients in the DSGb5 high expression group showed significantly lower recurrence-free survival as compared with those in the DSGb5 low expression group (log-rank P = 0.047). In the present study, DSGb5 expression was associated with microvascular invasion in RCC tissues, and patients with DSGb5 high expression showed significantly lower recurrence-free survival rates. These findings suggest that DSGb5 expressed in RCC is correlated with metastasis and is a potential predictor for identifying patients who experience metastasis after surgery.
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MESH Headings
- Aged
- Antibodies, Monoclonal, Murine-Derived/chemistry
- Antineoplastic Agents, Immunological/chemistry
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/mortality
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/surgery
- Disease-Free Survival
- Female
- Gene Expression Regulation, Neoplastic
- Globosides/biosynthesis
- Humans
- Immunohistochemistry
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/mortality
- Kidney Neoplasms/pathology
- Kidney Neoplasms/surgery
- Kidney Tubules, Distal/metabolism
- Kidney Tubules, Distal/pathology
- Male
- Middle Aged
- Neoplasm Metastasis
- Survival Rate
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Affiliation(s)
- Jun Itoh
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Akihiro Ito
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan.
| | - Shuichi Shimada
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Yoshihide Kawasaki
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Narihiko Kakoi
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Hideo Saito
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Koji Mitsuzuka
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Mika Watanabe
- Department of Pathology, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Makoto Satoh
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Seiichi Saito
- Department of Urology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Yoichi Arai
- Department of Urology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
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Sporadic Trichoblastomas and Those Occurring in the Setting of Multiple Familial Trichoepithelioma/Brooke-Spiegler Syndrome Show No BAP1 Loss. Am J Dermatopathol 2017; 39:793-794. [PMID: 28098597 DOI: 10.1097/dad.0000000000000763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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He X, Sun F, Guo F, Wang K, Gao Y, Feng Y, Song B, Li W, Li Y. Knockdown of Long Noncoding RNA FTX Inhibits Proliferation, Migration, and Invasion in Renal Cell Carcinoma Cells. Oncol Res 2016; 25:157-166. [PMID: 27983937 PMCID: PMC7840817 DOI: 10.3727/096504016x14719078133203] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC) is one of the most common kidney cancers worldwide. Although great progressions have been made in the past decades, its morbidity and lethality remain increasing. Long noncoding RNAs (lncRNAs) are demonstrated to play significant roles in the tumorigenesis. This study aimed to investigate the detailed roles of lncRNA FTX in RCC cell proliferation and metastasis. Our results showed that the transcript levels of FTX in both clinical RCC tissues and the cultured RCC cells were significantly upregulated and associated with multiple clinical parameters of RCC patients, including familial status, tumor sizes, lymphatic metastasis, and TNM stages. With cell proliferation assays, colony formation assays, and cell cycle assays, we testified that knockdown of FTX in A498 and ACHIN cells with specific shRNAs inhibited cell proliferation rate, colony formation ability, and arrested cell cycle in the G0/G1 phase. FTX depletion also suppressed cell migration and invasion with Transwell assays and wound-healing assays. These data indicated the pro-oncogenic potential of FTX in RCC, which makes it a latent therapeutic target of RCC diagnosis and treatment in the clinic.
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Affiliation(s)
- Xiangfei He
- Department of Urology, Linyi People's Hospital, Linyi City, Shandong Province, P.R. China
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