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Deng J, Tu S, Li L, Li G, Zhang Y. Diagnostic, predictive and prognostic molecular biomarkers in clear cell renal cell carcinoma: A retrospective study. Cancer Rep (Hoboken) 2024; 7:e2116. [PMID: 38837683 PMCID: PMC11150078 DOI: 10.1002/cnr2.2116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 02/05/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a common and aggressive subtype of kidney cancer. Many patients are diagnosed at advanced stages, making early detection crucial. Unfortunately, there are currently no noninvasive tests for ccRCC, emphasizing the need for new biomarkers. Additionally, ccRCC often develops resistance to treatments like radiotherapy and chemotherapy. Identifying biomarkers that predict treatment outcomes is vital for personalized care. The integration of artificial intelligence (AI), multi-omics analysis, and computational biology holds promise in bolstering detection precision and resilience, opening avenues for future investigations. The amalgamation of radiogenomics and biomaterial-basedimmunomodulation signifies a revolutionary breakthrough in diagnostic medicine. This review summarizes existing literature and highlights emerging biomarkers that enhance diagnostic, predictive, and prognostic capabilities for ccRCC, setting the stage for future clinical research.
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Affiliation(s)
- Jian Deng
- Department of OncologyHejiang Hospital of Traditional Chinese MedicineLuzhouPeople's Republic of China
- School of Basic Medical SciencesSouthwest Medical UniversityLuzhouPeople's Republic of China
| | - ShengYuan Tu
- School of Basic Medical SciencesSouthwest Medical UniversityLuzhouPeople's Republic of China
| | - Lin Li
- School of StomatologySouthwest Medical UniversityLuzhouPeople's Republic of China
| | - GangLi Li
- Department of OncologyHejiang Hospital of Traditional Chinese MedicineLuzhouPeople's Republic of China
| | - YinHui Zhang
- Department of PharmacyThe Affiliated Hospital of Southwest Medical UniversityLuzhouPeople's Republic of China
- Department of AnesthesiologyHospital (T.C.M) Affiliated to Southwest Medical UniversityLuzhouPeople's Republic of China
- Department of PharmacyHejiang Hospital of Traditional Chinese MedicineLuzhouPeople's Republic of China
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Gupta S, Kanwar SS. Biomarkers in renal cell carcinoma and their targeted therapies: a review. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:941-961. [PMID: 37970211 PMCID: PMC10645469 DOI: 10.37349/etat.2023.00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/21/2023] [Indexed: 11/17/2023] Open
Abstract
Renal cell carcinoma (RCC) is one of the most life-threatening urinary malignancies displaying poor response to radiotherapy and chemotherapy. Although in the recent past there have been tremendous advancements in using targeted therapies for RCC, despite that it remains the most lethal urogenital cancer with a 5-year survival rate of roughly 76%. Timely diagnosis is still the key to prevent the progression of RCC into metastatic stages as well as to treat it. But due to the lack of definitive and specific diagnostic biomarkers for RCC and its asymptomatic nature in its early stages, it becomes very difficult to diagnose it. Reliable and distinct molecular markers can not only refine the diagnosis but also classifies the tumors into thier sub-types which can escort subsequent management and possible treatment for patients. Potential biomarkers can permit a greater degree of stratification of patients affected by RCC and help tailor novel targeted therapies. The review summarizes the most promising epigenetic [DNA methylation, microRNA (miRNA; miR), and long noncoding RNA (lncRNA)] and protein biomarkers that have been known to be specifically involved in diagnosis, cancer progression, and metastasis of RCC, thereby highlighting their utilization as non-invasive molecular markers in RCC. Also, the rationale and development of novel molecular targeted drugs and immunotherapy drugs [such as tyrosine kinase inhibitors and immune checkpoint inhibitors (ICIs)] as potential RCC therapeutics along with the proposed implication of these biomarkers in predicting response to targeted therapies will be discussed.
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Affiliation(s)
- Shruti Gupta
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla 171 005, India
| | - Shamsher Singh Kanwar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla 171 005, India
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Molina-Cerrillo J, Santoni M, Ruiz Á, Massari F, Pozas J, Ortego I, Gómez V, Grande E, Alonso-Gordoa T. Epigenetics in advanced renal cell carcinoma: Potential new targets. Crit Rev Oncol Hematol 2022; 180:103857. [DOI: 10.1016/j.critrevonc.2022.103857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
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Rossi SH, Newsham I, Pita S, Brennan K, Park G, Smith CG, Lach RP, Mitchell T, Huang J, Babbage A, Warren AY, Leppert JT, Stewart GD, Gevaert O, Massie CE, Samarajiwa SA. Accurate detection of benign and malignant renal tumor subtypes with MethylBoostER: An epigenetic marker-driven learning framework. SCIENCE ADVANCES 2022; 8:eabn9828. [PMID: 36170366 PMCID: PMC9519038 DOI: 10.1126/sciadv.abn9828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Current gold standard diagnostic strategies are unable to accurately differentiate malignant from benign small renal masses preoperatively; consequently, 20% of patients undergo unnecessary surgery. Devising a more confident presurgical diagnosis is key to improving treatment decision-making. We therefore developed MethylBoostER, a machine learning model leveraging DNA methylation data from 1228 tissue samples, to classify pathological subtypes of renal tumors (benign oncocytoma, clear cell, papillary, and chromophobe RCC) and normal kidney. The prediction accuracy in the testing set was 0.960, with class-wise ROC AUCs >0.988 for all classes. External validation was performed on >500 samples from four independent datasets, achieving AUCs >0.89 for all classes and average accuracies of 0.824, 0.703, 0.875, and 0.894 for the four datasets. Furthermore, consistent classification of multiregion samples (N = 185) from the same patient demonstrates that methylation heterogeneity does not limit model applicability. Following further clinical studies, MethylBoostER could facilitate a more confident presurgical diagnosis to guide treatment decision-making in the future.
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Affiliation(s)
- Sabrina H. Rossi
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Izzy Newsham
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Sara Pita
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kevin Brennan
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Gahee Park
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Christopher G. Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Centre, Cambridge, UK
| | - Radoslaw P. Lach
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Mitchell
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Junfan Huang
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Babbage
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Y. Warren
- Department of Histopathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - John T. Leppert
- Department of Urology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Urology Surgical Service, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Olivier Gevaert
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Charles E. Massie
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Shamith A. Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
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Koudonas A, Papaioannou M, Kampantais S, Anastasiadis A, Hatzimouratidis K, Dimitriadis G. Methylation of PCDH17 and NEFH as prognostic biomarker for nonmetastatic RCC: A cohort study. Medicine (Baltimore) 2022; 101:e29599. [PMID: 35838992 PMCID: PMC11132415 DOI: 10.1097/md.0000000000029599] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/01/2022] [Indexed: 11/27/2022] Open
Abstract
DNA methylation makes up a main part of the molecular mechanism of cancer evolution and has shown promising results in the prognosis of renal cell cancer (RCC). In this study, we investigated the possible association of promoter methylation of PCDH17, NEFH, RASSF1A, and FHIT, genes with the prognosis of nonmetastatic RCC patients. Cancerous and normal adjacent tissues from surgical specimens of 41 patients with long follow-up were treated for DNA isolation and bisulfite conversion. The gene promoter methylation was determined with quantitative methylation-specific PCR (qMSP). Wilcoxon signed-rank test was used for paired methylation comparisons, while univariate linear regression and Mann-Whitney test were applied for associating methylation status with clinical and disease characteristics. Cox regression proportional hazards models and Kaplan-Meier plots were used for survival analyses in reference to methylation status. Paired comparisons showed tissue-specific hypermethylation for PCDH17 (P < .001), NEFH (P < .001), RASSF1A (P = .032), while a positive association of methylation in normal tissues with age was demonstrated for PCDH17 (P < .001), RASSF1A (P < .001), FHIT (P < .001). PCDH17 was more methylated in cases with clear cell RCC (P = .015) and high-grade tumor (P = .013), while NEFH methylation was higher in locally advanced cases (P = .032). PCDH17 hypermethylation in cancerous and normal tissues was linked to shorter disease-specific survival (DSS, P = .026, P = .004), disease-free survival (DFS, P = .004, P = .019) while NEFH hypermethylation in cancerous tissues was related to shorter DSS (P = .032). Increased methylation difference of NEFH was also associated with shorter DSS (P = .041) and DFS (P = .020), while the corresponding parameter for PCDH17 was associated with poor DFS (P = .014). Kaplan-Meier curves for hypermethylation in cancer tissues demonstrated different clinical courses for PCDH17 (P = .017), NEFH (P = .023) regarding DSS, and PCDH17 (P = .001) regarding DFS. Our study not only highlights the prognostic value of promoter methylation of PCDH17 and NEFH in cancer tissues but also is the first report of the prognostic value of methylation alterations in normal tissues. Our findings are the first report of the prognostic value of methylation alterations in normal tissues, which can contribute to improved assessment of recurrence risk.
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Affiliation(s)
- Antonios Koudonas
- First Department of Urology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Papaioannou
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Spyridon Kampantais
- First Department of Urology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasios Anastasiadis
- First Department of Urology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Georgios Dimitriadis
- First Department of Urology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Massen M, Lommen K, Wouters KAD, Vandersmissen J, van Criekinge W, Herman JG, Melotte V, Schouten LJ, van Engeland M, Smits KM. Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers. Clin Epigenetics 2022; 14:56. [PMID: 35477541 PMCID: PMC9047347 DOI: 10.1186/s13148-022-01273-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation biomarkers for early detection, risk stratification and treatment response in cancer have been of great interest over the past decades. Nevertheless, clinical implementation of these biomarkers is limited, as only < 1% of the identified biomarkers is translated into a clinical or commercial setting. Technical factors such as a suboptimal genomic location of the assay and inefficient primer or probe design have been emphasized as important pitfalls in biomarker research. Here, we use eleven diagnostic DNA methylation biomarkers for colorectal cancer (ALX4, APC, CDKN2A, MGMT, MLH1, NDRG4, SDC2, SFRP1, SFRP2, TFPI1 and VIM), previously described in a systematic literature search, to evaluate these pitfalls. Results To assess the genomic assay location, the optimal genomic locations according to TCGA data were extracted and compared to the genomic locations used in the published assays for all eleven biomarkers. In addition, all primers and probes were technically evaluated according to several criteria, based on literature and expert opinion. Both assay location and assay design quality varied widely among studies. Conclusions Large variation in both assay location and design hinders the development of future DNA methylation biomarkers as well as inter-study comparability.
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Affiliation(s)
- Maartje Massen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim Lommen
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim A D Wouters
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | | | - Wim van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, 9000, Ghent, Belgium
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15232, USA
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Leo J Schouten
- Department of Epidemiology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Kim M Smits
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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Gu Y, Yuan J. Diagnostic significance of miRNAs as potential biomarkers for human renal cell carcinoma: a systematic review and meta-analysis. Expert Rev Anticancer Ther 2022; 22:437-444. [PMID: 35255782 DOI: 10.1080/14737140.2022.2051483] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Numerous studies have explored miRNAs as potential diagnostic biomarkers in patients with renal cell carcinoma (RCC). However, its diagnostic accuracy remains controversial. RESEARCH DESIGN AND METHODS PubMed, Cochrane Library, Embase, Web of Science, China National Knowledge Infrastructure, China Science and Technology Journal, and Wanfang Databases were searched according to inclusion/exclusion criteria. The quality of the studies was assessed using the QUADAS-2 scale. The combined sensitivity, specificity, positive/negative likelihood ratios, diagnostic odds ratio, and area under the curve (AUC) of the summary receiver operating characteristic (SROC) were calculated using a bivariate mixed-effect model. RESULTS Of the 16 studies included, 20 diagnostic tests were assessed. Results are presented with a corresponding 95% confidence interval in brackets: for miR-210, the combined sensitivity was 0.78 (0.68-0.85), specificity 0.71 (0.61-0.79), and AUC 0.81 (0.77-0.8); for miR-378, combined sensitivity 0.78 (0.68-0.86), specificity 0.79 (0.64-0.89), and AUC 0.85 (0.81-0.88); for miR-1233, combined sensitivity 0.86 (0.80-0.90), specificity 0.80 (0.36-0.96), and AUC 0.86 (0.83-0.89); for miR-21, combined sensitivity 0.84 (0.78-0.89), specificity 0.79 (0.55-0.92), and AUC 0.87 (0.84-0.89). CONCLUSIONS This meta-analysis suggests that miR-210, miR-378, miR-1233, and miR-21 have high accuracy in diagnosing RCC.
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Affiliation(s)
- Yiwei Gu
- Department of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiuhong Yuan
- Department of Urology, West China Hospital, Sichuan University, Chengdu, China
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Epigenetic Biomarkers of Renal Cell Carcinoma for Liquid Biopsy Tests. Int J Mol Sci 2021; 22:ijms22168846. [PMID: 34445557 PMCID: PMC8396354 DOI: 10.3390/ijms22168846] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/06/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
Renal cell carcinomas (RCC) account for 2–3% of the global cancer burden and are characterized by the highest mortality rate among all genitourinary cancers. However, excluding conventional imagining approaches, there are no reliable diagnostic and prognostic tools available for clinical use at present. Liquid biopsies, such as urine, serum, and plasma, contain a significant amount of tumor-derived nucleic acids, which may serve as non-invasive biomarkers that are particularly useful for early cancer detection, follow-up, and personalization of treatment. Changes in epigenetic phenomena, such as DNA methylation level, expression of microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), are observed early during cancer development and are easily detectable in biofluids when morphological changes are still undetermined by conventional diagnostic tools. Here, we reviewed recent advances made in the development of liquid biopsy-derived DNA methylation-, miRNAs- and lncRNAs-based biomarkers for RCC, with an emphasis on the performance characteristics. In the last two decades, a mass of circulating epigenetic biomarkers of RCC were suggested, however, most of the studies done thus far analyzed biomarkers selected from the literature, used relatively miniature, local, and heterogeneous cohorts, and suffered from a lack of sufficient validations. In summary, for improved translation into the clinical setting, there is considerable demand for the validation of the existing pool of RCC biomarkers and the discovery of novel ones with better performance and clinical utility.
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A 25-year perspective on evaluation and understanding of biomarkers in urologic cancers. Urol Oncol 2021; 39:602-617. [PMID: 34315659 DOI: 10.1016/j.urolonc.2021.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/15/2022]
Abstract
The past 25 years have witnessed an explosion of investigative attempts to identify clinically useful biomarkers which can have meaningful impacts for patients with urologic cancers. However, in spite of the enormous amount of research aiming to identify markers with the hope of impacting patient care, only a handful have proven to have true clinical utility. Improvements in targeted imaging, pan-omics evaluation, and genetic sequencing at the tissue and single-cell levels have yielded many potential targets for continued biomarker investigation. This article, as one in this series for the 25th Anniversary Issue of Urologic Oncology: Seminars and Original Investigations, serves to give a perspective on our progress and failures over the past quarter-century in our highest volume urologic cancers: prostate, bladder, and kidney cancers.
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The Role of Epigenetics in the Progression of Clear Cell Renal Cell Carcinoma and the Basis for Future Epigenetic Treatments. Cancers (Basel) 2021; 13:cancers13092071. [PMID: 33922974 PMCID: PMC8123355 DOI: 10.3390/cancers13092071] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The accumulated evidence on the role of epigenetic markers of prognosis in clear cell renal cell carcinoma (ccRCC) is reviewed, as well as state of the art on epigenetic treatments for this malignancy. Several epigenetic markers are likely candidates for clinical use, but still have not passed the test of prospective validation. Development of epigenetic therapies, either alone or in combination with tyrosine-kinase inhibitors of immune-checkpoint inhibitors, are still in their infancy. Abstract Clear cell renal cell carcinoma (ccRCC) is curable when diagnosed at an early stage, but when disease is non-confined it is the urologic cancer with worst prognosis. Antiangiogenic treatment and immune checkpoint inhibition therapy constitute a very promising combined therapy for advanced and metastatic disease. Many exploratory studies have identified epigenetic markers based on DNA methylation, histone modification, and ncRNA expression that epigenetically regulate gene expression in ccRCC. Additionally, epigenetic modifiers genes have been proposed as promising biomarkers for ccRCC. We review and discuss the current understanding of how epigenetic changes determine the main molecular pathways of ccRCC initiation and progression, and also its clinical implications. Despite the extensive research performed, candidate epigenetic biomarkers are not used in clinical practice for several reasons. However, the accumulated body of evidence of developing epigenetically-based biomarkers will likely allow the identification of ccRCC at a higher risk of progression. That will facilitate the establishment of firmer therapeutic decisions in a changing landscape and also monitor active surveillance in the aging population. What is more, a better knowledge of the activities of chromatin modifiers may serve to develop new therapeutic opportunities. Interesting clinical trials on epigenetic treatments for ccRCC associated with well established antiangiogenic treatments and immune checkpoint inhibitors are revisited.
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DNA methylation profiling reveals new potential subtype-specific gene markers for early-stage renal cell carcinoma in caucasian population. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kołat D, Kałuzińska Ż, Orzechowska M, Bednarek AK, Płuciennik E. Functional genomics of AP-2α and AP-2γ in cancers: in silico study. BMC Med Genomics 2020; 13:174. [PMID: 33213447 PMCID: PMC7678100 DOI: 10.1186/s12920-020-00823-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/12/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Among all causes of death, cancer is the most prevalent and is only outpaced by cardiovascular diseases. Molecular theory of carcinogenesis states that apoptosis and proliferation are regulated by groups of tumor suppressors or oncogenes. Transcription factors are example of proteins comprising representatives of both cancer-related groups. Exemplary family of transcription factors which exhibits dualism of function is Activating enhancer-binding Protein 2 (AP-2). Scientific reports concerning their function in carcinogenesis depend on particular family member and/or tumor type which proves the issue to be unsolved. Therefore, the present study examines role of the best-described AP-2 representatives, AP-2α and AP-2γ, through ontological analysis of their target genes and investigation what processes are differentially regulated in 21 cancers using samples deposited in Genomic Data Analysis Center (GDAC) Firehose. METHODS Expression data with clinical annotation was collected from TCGA-dedicated repository GDAC Firehose. Transcription factor targets were obtained from Gene Transcription Regulation Database (GTRD), TRANScription FACtor database (TRANSFAC) and Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRRUST). Monocle3 R package was used for global samples profiling while Protein ANalysis THrough Evolutionary Relationships (PANTHER) tool was used to perform gene ontology analysis. RESULTS With RNA-seq data and Monocle3 or PANTHER tools we outlined differences in many processes and signaling pathways, separating tumor from normal tissues or tumors from each other. Unexpectedly, a number of alterations in basal-like breast cancer were identified that distinguished it from other subtypes, which could bring future clinical benefits. CONCLUSIONS Our findings indicate that while the AP-2α/γ role remains ambiguous, their activity is based on processes that underlie the cancer hallmarks and their expression could have potential in diagnosis of selected tumors.
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Affiliation(s)
- Damian Kołat
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland.
| | - Żaneta Kałuzińska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Magdalena Orzechowska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
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Biobanking in Molecular Biomarker Research for the Early Detection of Cancer. Cancers (Basel) 2020; 12:cancers12040776. [PMID: 32218259 PMCID: PMC7226426 DOI: 10.3390/cancers12040776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/23/2022] Open
Abstract
Although population-wide screening programs for several cancer types have been implemented in multiple countries, screening procedures are invasive, time-consuming and often perceived as a burden for patients. Molecular biomarkers measurable in non-invasively collected samples (liquid biopsies) could facilitate screening, as they could have incremental value on early diagnosis of cancer, but could also predict prognosis or monitor treatment response. Although the shift towards biomarkers from liquid biopsies for early cancer detection was initiated some time ago, there are many challenges that hamper the development of such biomarkers. One of these challenges is large-scale validation that requires large prospectively collected biobanks with liquid biopsies. Establishing those biobanks involves several considerations, such as standardization of sample collection, processing and storage within and between biobanks. In this perspective, we will elaborate on several issues that need to be contemplated in biobanking, both in general and for certain specimen types specifically, to be able to facilitate biomarker validation for early detection of cancer.
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