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Kalinkin AI, Sigin VO, Kuznetsova EB, Ignatova EO, Vinogradov II, Vinogradov MI, Vinogradov IY, Zaletaev DV, Nemtsova MV, Kutsev SI, Tanas AS, Strelnikov VV. Epigenomic Profiling Advises Therapeutic Potential of Leukotriene Receptor Inhibitors for a Subset of Triple-Negative Breast Tumors. Int J Mol Sci 2023; 24:17343. [PMID: 38139172 PMCID: PMC10743620 DOI: 10.3390/ijms242417343] [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: 11/01/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive molecular subtype, with a poor survival rate compared to others subtypes. For a long time, chemotherapy was the only systemic treatment for TNBC, and the identification of actionable molecular targets might ultimately improve the prognosis for TNBC patients. We performed a genome-wide analysis of DNA methylation at CpG islands on a collection of one hundred ten breast carcinoma samples and six normal breast tissue samples using reduced representation bisulfite sequencing with the XmaI restriction enzyme (XmaI-RRBS) and identified a subset of TNBC samples with significant hypomethylation at the LTB4R/LTB4R2 genes' CpG islands, including CpG dinucleotides covered with cg12853742 and cg21886367 HumanMethylation 450K microarray probes. Abnormal DNA hypomethylation of this region in TNBC compared to normal samples was confirmed by bisulfite Sanger sequencing. Gene expression generally anticorrelates with promoter methylation, and thus, the promoter hypomethylation detected and confirmed in our study might be revealed as an indirect marker of high LTB4R/LTB4R2 expression using a simple methylation-sensitive PCR test. Analysis of RNA-seq expression and DNA methylation data from the TCGA dataset demonstrates that the expression of the LTB4R and LTB4R2 genes significantly negatively correlates with DNA methylation at both CpG sites cg12853742 (R = -0.4, p = 2.6 × 10-6; R = -0.21, p = 0.015) and cg21886367 (R = -0.45, p = 7.3 × 10-8; R = -0.24, p = 0.005), suggesting the upregulation of these genes in tumors with abnormal hypomethylation of their CpG island. Kaplan-Meier analysis using the TCGA-BRCA gene expression and clinical data revealed poorer overall survival for TNBC patients with an upregulated LTB4R. To this day, only the leukotriene inhibitor LY255283 has been tested on an MCF-7/DOX cell line, which is a luminal A breast cancer molecular subtype. Other studies compare the effects of Montelukast and Zafirlukast (inhibitors of the cysteinyl leukotriene receptor, which is different from LTB4R/LTB4R2) on the MDA-MB-231 (TNBC) cell line, with high methylation and low expression levels of LTB4R. In our study, we assess the therapeutic effects of various drugs (including leukotriene receptor inhibitors) with the DepMap gene effect and drug sensitivity data for TNBC cell lines with hypomethylated and upregulated LTB4R/LTB4R2 genes. LY255283, Minocycline, Silibinin, Piceatannol, Mitiglinide, 1-Azakenpaullone, Carbetocin, and Pim-1-inhibitor-2 can be considered as candidates for the additional treatment of TNBC patients with tumors demonstrating LTB4R/LTB4R2 hypomethylation/upregulation. Finally, our results suggest that the epigenetic status of leukotriene B4 receptors is a novel, potential, predictive, and prognostic biomarker for TNBC. These findings might improve individualized therapy for TNBC patients by introducing new therapeutic adjuncts as anticancer agents.
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Affiliation(s)
- Alexey I. Kalinkin
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
| | - Vladimir O. Sigin
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
| | - Ekaterina B. Kuznetsova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| | - Ekaterina O. Ignatova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
- Nikolay Nikolaevich Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia
| | - Ilya I. Vinogradov
- Regional Clinical Oncology Dispensary, 390011 Ryazan, Russia;
- Department of Histology, Pathological Anatomy and Medical Genetics, Ryazan State Medical University, 390026 Ryazan, Russia; (M.I.V.); (I.Y.V.)
| | - Maxim I. Vinogradov
- Department of Histology, Pathological Anatomy and Medical Genetics, Ryazan State Medical University, 390026 Ryazan, Russia; (M.I.V.); (I.Y.V.)
| | - Igor Y. Vinogradov
- Department of Histology, Pathological Anatomy and Medical Genetics, Ryazan State Medical University, 390026 Ryazan, Russia; (M.I.V.); (I.Y.V.)
| | - Dmitry V. Zaletaev
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
| | - Marina V. Nemtsova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| | - Sergey I. Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
| | - Alexander S. Tanas
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
| | - Vladimir V. Strelnikov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (V.O.S.); (E.B.K.); (E.O.I.); (D.V.Z.); (M.V.N.); (S.I.K.); (A.S.T.); (V.V.S.)
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Shlyapnikov YM, Malakhova EA, Vinarov AZ, Potoldykova NV, Vladimirov VI, Zernii EY, Zamyatnin AA, Shlyapnikova EA. Cancer-Retina Antigens in the Urine of Bladder and Prostate Cancer Patients. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1268-1276. [PMID: 36509724 DOI: 10.1134/s0006297922110062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
It has recently been shown that combination of arrestin and recoverin can serve as an effective urinary biomarker for renal cell carcinoma with sensitivity and specificity of over 92%. In this work, we studied the possibility of detecting these antigens in the urine in other urological oncological diseases - bladder cancer (BC) and prostate cancer (PCa). Urine samples from 40 BC patients and 40 PCa patients were analyzed using an ultrasensitive microarray immunoassay with a detection limit of 0.1 pg/ml. It was shown that in BC the sensitivity of determining combination of arrestin with recoverin is 58% (AUC 0.76, 95% CI 0.66-0.86), while in PCa it is 60% (AUC 0.7, 95% CI 0.68-0.88). It has been established that in patients with bladder and prostate cancer who had a positive test, these antigens are not detected in 90% of cases after removal of the tumor. In the future, the obtained results could become the basis for developing new approaches for timely detection of relapses of such diseases and treatment control, as well as for the development of new diagnostic methods.
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Affiliation(s)
- Yuri M Shlyapnikov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290, Russia.
| | - Ekaterina A Malakhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Andrey Z Vinarov
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Natalia V Potoldykova
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Vasiliy I Vladimirov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117437, Russia
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Andrey A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.,Department of Biotechnology, Sirius University of Science and Technology, Krasnodar Region, Federal Territory Sirius, 354340, Russia
| | - Elena A Shlyapnikova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290, Russia
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Shlyapnikov YM, Malakhova EA, Potoldykova NV, Svetocheva YA, Vinarov AZ, Zinchenko DV, Zernii EY, Zamyatnin AA, Shlyapnikova EA. Non-Invasive Diagnostics of Renal Cell Carcinoma Using Ultrasensitive Immunodetection of Cancer-Retina Antigens. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:658-666. [PMID: 36154884 DOI: 10.1134/s0006297922070070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/06/2022] [Accepted: 06/15/2022] [Indexed: 06/16/2023]
Abstract
Renal cell carcinoma (RCC) is the most common urological malignancy with a high mortality and low detection rate. One of the approaches to improving its diagnostics may be the search for new non-invasive biomarkers in liquid biopsy and development of more sensitive methods for their detection. Cancer-retina antigens, which are known to be aberrantly expressed in malignant tumors, are present in liquid biopsy at extremely low concentrations. Using the developed multiplex immunoassay with a detection limit of 0.1 pg/ml, urine and serum samples of 89 patients with RCC and 50 non-cancer patients were examined for the presence of cancer-retina antigens (arrestin, recoverin, rhodopsin kinase, and transducin); the difference between the RCC and control groups was evaluated with the χ2 test. The results showed high diagnostic efficiency of a combination of arrestin and recoverin: at a threshold of 0.1 pg/ml, the sensitivity was 96%, specificity 92%, and AUC = 0.96 (95% confidence interval, 0.93-0.99). Seven days after nephrectomy, the concentration of the antigens returned to the level characteristic of the control group. Therefore, arrestin in a combination with recoverin can serve as a diagnostic non-invasive urinary biomarker of RCC.
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Affiliation(s)
- Yuri M Shlyapnikov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Ekaterina A Malakhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Natalia V Potoldykova
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Yana A Svetocheva
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Andrei Z Vinarov
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 117997, Russia.
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Andrey A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
- Department of Biotechnology, Sirius University of Science and Technology, Sochi, 354340, Russia
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Elena A Shlyapnikova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Shlyapnikov YM, Malakhova EA, Vinarov AZ, Zamyatnin AA, Shlyapnikova EA. Can new immunoassay techniques improve bladder cancer diagnostics With protein biomarkers? Front Mol Biosci 2021; 7:620687. [PMID: 33659273 PMCID: PMC7917292 DOI: 10.3389/fmolb.2020.620687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
The search for new diagnostic tests for cancer or ways to improve existing tests is primarily driven by the desire to identify the disease as early as possible. In this report, we summarize the current knowledge of the most promising diagnostic protein bladder cancer (BC) markers reported over the last decade. Unfortunately, analysis of published data suggests that a reliable, highly sensitive biomarker test-system based on ELISA for detecting BC has not yet been developed. The use of more sensitive assays to detect ultra-low concentrations of biomarkers not available for ELISA, could be very beneficial. Based on the literature and pilot experimental data, we conclude that a highly sensitive immunoassay using microarrays and magnetic labels, could be an effective and cheap technique suitable for the detection of diagnostically relevant BC biomarkers.
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Affiliation(s)
- Yuri M Shlyapnikov
- Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Russia
| | | | - Andrey Z Vinarov
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Andrey A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia.,Department of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
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Wagley S, Tran TM, Mallory PW, Lee MS, Armbrust KR, Trautman B, Montezuma SR. Cancer-Associated Retinopathy due to Clear Cell Renal Carcinoma. Ocul Oncol Pathol 2020; 7:31-35. [PMID: 33796514 DOI: 10.1159/000511189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/21/2020] [Indexed: 11/19/2022] Open
Abstract
An 84-year-old female presented with bilateral scotomas and progressive nyctalopia over 1 year. Best-corrected visual acuity was 20/50 in both eyes with reduced color vision. Goldmann visual field showed bilateral cecocentral scotomas and generalized constriction of the visual fields. This led to an electroretinogram showing an electronegative pattern consistent with autoimmune retinopathies. Infectious workup was negative. Anti-retinal antibodies were positive, leading to a presumed diagnosis of cancer-associated retinopathy (CAR). Imaging showed a previously unknown left renal lower pole mass, and she underwent a radical nephrectomy. Biopsy showed nuclear grade-3 clear cell renal carcinoma staged T1. The patient was treated with oral prednisone with no ocular improvement. We report on a rare case of clear cell renal carcinoma causing CAR. CAR is an important paraneoplastic syndrome to diagnose since the majority of ocular cases precede other manifestations of malignancy. Therefore, a timely diagnosis of CAR can be lifesaving or at least life-extending.
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Affiliation(s)
- Sushant Wagley
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tu M Tran
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Paul W Mallory
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael S Lee
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Bruce Trautman
- Anatomic Pathology, Fairview Southdale Hospital, Edina, Minnesota, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
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Wang YL, Zhang YY. cg04448376, cg24387542, cg08548498, and cg14621323 as a Novel Signature to Predict Prognosis in Kidney Renal Papillary Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4854390. [PMID: 33381555 PMCID: PMC7759405 DOI: 10.1155/2020/4854390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/19/2020] [Accepted: 11/28/2020] [Indexed: 10/26/2022]
Abstract
INTRODUCTION DNA methylation plays a vital role in prognosis prediction of cancers. In this study, we aimed to identify novel DNA methylation site biomarkers and create an efficient methylated site model for predicting survival in kidney renal papillary cell carcinoma (KIRP). METHODS DNA methylation and gene expression profile data were downloaded from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Differential methylated genes (DMGs) and differential expression genes (DEGs) were identified and then searched for the hub genes. Cox proportional hazards regression was applied to identify DNA methylated site biomarkers from the hub genes. Kaplan-Meier survival and ROC analyses were used to validate the effective prognostic ability of the methylation gene site biomarker. The biomarker sites were validated in the GEO cohorts. The GO and KEGG annotation was done to explore the biological function of DNA methylated site signature. RESULTS Nine DMGs with opposite expression patterns containing 47 methylated sites were identified. Finally, four methylated sites were identified using the hazard regression model (cg04448376, cg24387542, cg08548498, and cg14621323) located in UTY, LGALS9B, SLPI, and PFN3, respectively. These sites classified patients into high- and low-risk groups in the training cohort. The 5-year survival rates for patients with low-risk and high-risk scores were 97.5% and 75.9% (P < 0.001). The prognostic accuracy and signature methylation sites were validated in the test (TCGA, n = 87) and GEO cohorts (n = 14). Multivariate regression analysis showed that the signature was an independent prediction prognostic factor for KIRP. Based on this analysis, we developed methylated site signature nomogram that predicts an individual's risk of survival. Functional analysis suggested that these signature genes are involved in the biological processes of protein binding. CONCLUSIONS Our study demonstrated that the methylated gene site signature might be a powerful prognostic tool for evaluating survival rate and guiding tailored therapy for KIRP patients.
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Affiliation(s)
- Ying-Lei Wang
- Department of Urinary Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, China
| | - Ying-Ying Zhang
- Out-patient Department, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, China
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Dong M, Yang Z, Li X, Zhang Z, Yin A. Screening of Methylation Gene Sites as Prognostic Signature in Lung Adenocarcinoma. Yonsei Med J 2020; 61:1013-1023. [PMID: 33251775 PMCID: PMC7700873 DOI: 10.3349/ymj.2020.61.12.1013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/05/2020] [Accepted: 10/18/2020] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Most lung adenocarcinoma (LUAD) patients are diagnosed at the advanced stage and have poor prognosis. DNA methylation plays an important role in the prognosis prediction of cancers. The objective of this study was to identify new DNA methylation sites as biomarkers for LUAD prognosis. MATERIALS AND METHODS We downloaded DNA methylation data from The Cancer Genome Atlas data portal. Cox proportional hazard regression model and random survival forest algorithm were applied to identify the DNA-methylation sites. Methylation of sites were validated in the Gene Expression Omnibus cohorts. Function annotation were done to explore the biological function of DNA methylated sites signature. RESULTS Six DNA methylation sites were identified as prognosis signature. The signature yielded acceptable discrimination between the high-risk group and low-risk group. The discrimination effect of this DNA methylation signature for the OS was obvious, with a median OS of 21.89 months vs. 17.74 months for high-risk vs. low-risk groups. This prognostic prediction model was validated by the test group and GEO dataset. The predictive survival value was higher for the prognostic prediction model than that for the tumor node metastasis stage. Adjuvant hemotherapy could not affect the prediction of the signature. Functional analysis indicated that these signature genes were involved in protein binding and cytoplasm. CONCLUSION We identified the prognostic signature for LUAD by combining six DNA methylation sites. This could service as potential robust and specificity signature in the prognosis prediction of LUAD.
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Affiliation(s)
- Min Dong
- Pulmonology Respiratory and Critical Care Unit, Gansu Province Hospital of Traditional Chinese Medicine, Lanzhou, China
| | - Zengli Yang
- Infectious Diseases Unit, First People's Hospital of Guannan County, Guannan, China
| | - Xingfang Li
- Pulmonology Respiratory and Critical Care Unit, Gansu Province Hospital of Traditional Chinese Medicine, Lanzhou, China
| | - Zhenxiang Zhang
- Orthopedics, Lanzhou Traditional Chinese Medicine Hospital, Lanzhou, China
| | - Ankang Yin
- Department of General Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, China.
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Prognostic Value of DNA Methylation-Driven Genes in Clear Cell Renal Cell Carcinoma: A Study Based on Methylation and Transcriptome Analyses. DISEASE MARKERS 2020; 2020:8817652. [PMID: 32733620 PMCID: PMC7369658 DOI: 10.1155/2020/8817652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/15/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022]
Abstract
Background Few previous studies have comprehensively explored the level of DNA methylation and gene expression in ccRCC. The purpose of this study was to identify the key clear cell renal cell carcinoma- (ccRCC-) related DNA methylation-driven genes (MDG) and to build a prognostic model based on the level of DNA methylation. Methods RNA-seq transcriptome data and DNA methylation data were obtained from The Cancer Genome Atlas. Based on the MethylMix algorithm, we obtain ccRCC-related MDG. The univariate and multivariate Cox regression analyses were employed to investigate the correlation between patient overall survival and the methylation level of each MDG. Finally, a prognosis risk score was established based on a linear combination of the regression coefficient derived from the multivariate Cox regression model (β) multiplied with the methylation level of the gene. Results 19 ccRCC-related MDG were identified. Three MDG (NCKAP1L, EVI2A, and BATF) were further screened and integrated into a prognostic risk score model, risk score = (3.710∗methylation level of NCKAP1L) + (-3.892∗methylation level of EVI2A) + (-3.907∗methylation level of BATF). The risk model was independent from conventional clinical characteristics as a prognostic factor for ccRCC (HR = 1.221, 95% confidence interval: 1.063-1.402, and P = 0.005). The joint survival analysis showed that the gene expression and methylation levels of the prognostic genes EVI2A and BATF were significantly related with prognosis. Conclusion This study provided an important bioinformatics foundation for in-depth studies of ccRCC DNA methylation.
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Peters I, Merseburger AS, Tezval H, Lafos M, Tabrizi PF, Mazdak M, Wolters M, Kuczyk MA, Serth J, von Klot CA. The Prognostic Value of DNA Methylation Markers in Renal Cell Cancer: A Systematic Review. KIDNEY CANCER 2020. [DOI: 10.3233/kca-190069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | | | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mehrdad Mazdak
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mathias Wolters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
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Baldin AV, Savvateeva LV, Bazhin AV, Zamyatnin AA. Dendritic Cells in Anticancer Vaccination: Rationale for Ex Vivo Loading or In Vivo Targeting. Cancers (Basel) 2020; 12:cancers12030590. [PMID: 32150821 PMCID: PMC7139354 DOI: 10.3390/cancers12030590] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Dendritic cells (DCs) have shown great potential as a component or target in the landscape of cancer immunotherapy. Different in vivo and ex vivo strategies of DC vaccine generation with different outcomes have been proposed. Numerous clinical trials have demonstrated their efficacy and safety in cancer patients. However, there is no consensus regarding which DC-based vaccine generation method is preferable. A problem of result comparison between trials in which different DC-loading or -targeting approaches have been applied remains. The employment of different DC generation and maturation methods, antigens and administration routes from trial to trial also limits the objective comparison of DC vaccines. In the present review, we discuss different methods of DC vaccine generation. We conclude that standardized trial designs, treatment settings and outcome assessment criteria will help to determine which DC vaccine generation approach should be applied in certain cancer cases. This will result in a reduction in alternatives in the selection of preferable DC-based vaccine tactics in patient. Moreover, it has become clear that the application of a DC vaccine alone is not sufficient and combination immunotherapy with recent advances, such as immune checkpoint inhibitors, should be employed to achieve a better clinical response and outcome.
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Affiliation(s)
- Alexey V. Baldin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.V.B.); (L.V.S.)
| | - Lyudmila V. Savvateeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.V.B.); (L.V.S.)
| | - Alexandr V. Bazhin
- Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians University of Munich, 81377 Munich, Germany;
- German Cancer Consortium (DKTK), Partner Site Munich, 80336 Munich, Germany
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.V.B.); (L.V.S.)
- Belozersky Institute of Physico-Chemical Biology, Department of Cell Signaling, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: ; Tel.: +74-956-229-843
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Liu Y, Zhang Z, Li T, Li X, Zhang S, Li Y, Zhao W, Gu Y, Guo Z, Qi L. A Qualitative Transcriptional Signature for Predicting Recurrence Risk for High-Grade Serous Ovarian Cancer Patients Treated With Platinum-Taxane Adjuvant Chemotherapy. Front Oncol 2019; 9:1094. [PMID: 31681618 PMCID: PMC6813654 DOI: 10.3389/fonc.2019.01094] [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: 04/19/2019] [Accepted: 10/04/2019] [Indexed: 11/13/2022] Open
Abstract
Resistance to platinum and taxane adjuvant chemotherapy (ACT) is the main cause of the recurrence and poor prognosis of high-grade serous ovarian cancer (HGS-OvCa) patients receiving platinum-taxane ACT after surgery. However, currently reported quantitative transcriptional signatures, which are commonly based on risk scores summarized from gene expression, are unsuitable for clinical application because of their high sensitivity to experimental batch effects and quality uncertainties of clinical samples. Using 226 samples of HGS-OvCa patients receiving platinum-taxane ACT in TCGA, we developed a qualitative transcriptional signature, consisting of four gene pairs whose within-samples relative expression orderings could robustly predict patient recurrence-free survival (RFS). In two independent test datasets, the predicted non-responders had significantly shorter RFS than the predicted responders (log-rank p < 0.05). In a test dataset containing data for patient pathological response state, the signature reclassified 12 out of 22 pathological complete response patients as non-responders and two out of 16 pathological non-complete response patients as responders. Notably, the 12 predicted non-responders in the pathological complete response group had significantly shorter RFS than the predicted responders (log-rank p = 0.0122). This qualitative transcriptional signature, which is insensitive to experimental batch effects and quality uncertainties of clinical samples, can individually identify HGS-OvCa patients who are more likely to benefit from platinum-taxane adjuvant chemotherapy.
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Affiliation(s)
- Yixin Liu
- Basic Medicine College, Harbin Medical University, Harbin, China
| | - Zheyang Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tianhao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ying Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenyuan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunyan Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zheng Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Lishuang Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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12
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Baldin AV, Zamyatnin AA, Bazhin AV, Xu WH, Savvateeva LV. Advances in the Development of Anticancer HSP-based Vaccines. Curr Med Chem 2019; 26:427-445. [PMID: 29376489 DOI: 10.2174/0929867325666180129100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/11/2017] [Accepted: 01/01/2018] [Indexed: 01/01/2023]
Abstract
Current advances in cancer treatment are based on the recent discoveries of molecular mechanisms of tumour maintenance. It was shown that heat shock proteins (HSPs) play a crucial role in the development of immune response against tumours. Thus, HSPs represent multifunctional agents not only with chaperone functions, but also possessing immunomodulatory properties. These properties are exploited for the development of HSP-based anticancer vaccines aimed to induce cytotoxic responses against tumours. To date, a number of strategies have been suggested to facilitate HSP-based vaccine production and to increase its effectiveness. The present review focuses on the current trend for the development of HSPbased vaccines aimed at inducing strong immunological tumour-specific responses against cancer cells of distinct etiology and localization.
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Affiliation(s)
- Alexey V Baldin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russian Federation.,Lomonosov Moscow State University, Department of Cell Signaling, Belozersky Institute of Physico- Chemical Biology, 119991, Moscow, Russian Federation
| | - Alexandr V Bazhin
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Germany
| | - Wan-Hai Xu
- Department of Urology, the Fourth Hospital of Harbin Medical University, Harbin, China
| | - Lyudmila V Savvateeva
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russian Federation
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13
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Tanas AS, Sigin VO, Kalinkin AI, Litviakov NV, Slonimskaya EM, Ibragimova MK, Ignatova EO, Simonova OA, Kuznetsova EB, Kekeeva TV, Larin SS, Poddubskaya EV, Trotsenko ID, Rudenko VV, Karandasheva KO, Petrova KD, Tsyganov MM, Deryusheva IV, Kazantseva PV, Doroshenko AV, Tarabanovskaya NA, Chesnokova GG, Sekacheva MI, Nemtsova MV, Izhevskaya VL, Kutsev SI, Zaletaev DV, Strelnikov VV. Genome-wide methylotyping resolves breast cancer epigenetic heterogeneity and suggests novel therapeutic perspectives. Epigenomics 2019; 11:605-617. [PMID: 30729807 DOI: 10.2217/epi-2018-0213] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To provide a breast cancer (BC) methylotype classification by genome-wide CpG islands bisulfite DNA sequencing. Materials & methods: XmaI-reduced representation bisulfite sequencing DNA methylation sequencing method was used to profile DNA methylation of 110 BC samples and 6 normal breast samples. Intrinsic DNA methylation BC subtypes were elicited by unsupervised hierarchical cluster analysis, and cluster-specific differentially methylated genes were identified. Results & conclusion: Overall, six distinct BC methylotypes were identified. BC cell lines constitute a separate group extremely highly methylated at the CpG islands. In turn, primary BC samples segregate into two major subtypes, highly and moderately methylated. Highly and moderately methylated superclusters, each incorporate three distinct epigenomic BC clusters with specific features, suggesting novel perspectives for personalized therapy.
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Affiliation(s)
- Alexander S Tanas
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vladimir O Sigin
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Alexey I Kalinkin
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Nikolai V Litviakov
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Elena M Slonimskaya
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Marina K Ibragimova
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Ekaterina O Ignatova
- Clinical Pharmacology & Chemotherapy, Federal State Budgetary institution «N.N. Blokhin National Medical Research Center of Oncology» of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga A Simonova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Tatiana V Kekeeva
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Sergey S Larin
- Gene Therapy Laboratory, Institute of Gene Biology, Moscow, Russia.,Molecular Immunology Laboratory, Federal Scientific Clinical Centre of Pediatric Hematology Oncology Immunology Named after Dmitry Rogachev, Moscow, Russia
| | - Elena V Poddubskaya
- Clinic of Personalized Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,VitaMed LLC, Moscow, Russia
| | | | - Viktoria V Rudenko
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | | | - Kseniya D Petrova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics & Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Matvey M Tsyganov
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Irina V Deryusheva
- Laboratory of Oncovirology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Polina V Kazantseva
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Artem V Doroshenko
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Natalia A Tarabanovskaya
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Tomsk, Russia
| | - Galina G Chesnokova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Marina I Sekacheva
- Clinic of Personalized Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Marina V Nemtsova
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Vera L Izhevskaya
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Sergey I Kutsev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry V Zaletaev
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia.,Medical Genetics Laboratory, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Vladimir V Strelnikov
- Epigenetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia.,Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, Moscow, Russia
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14
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Kochurova EV. Comparative Role of Matrixins in Diagnostics of Parotid Gland Tumors. Bull Exp Biol Med 2019; 166:383-385. [PMID: 30617705 DOI: 10.1007/s10517-019-04355-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 10/27/2022]
Abstract
The benign and malignant neoplasms in parotid gland have similar clinical presentations despite different tumor growth rates. The study compared the clinical and morphological data as well as the results of ELISA for MMP-2, MMP-8, MMP-9, TIMP-1, and TIMP-2 in salivary fluid yielded during primary examination of the patients with pleomorphic adenoma and adenocarcinoma of parotid gland. The examined biomarkers detected in salivary fluid in patients with various cancer types differed significantly (p≤0.05). The correlations between clinical identification of adenoma or adenocarcinoma, on the one hand, and the levels of MMP-8, TIMP-1, and TIMP-2, on the other hand, makes it possible to use the latter as biomarkers for early detection and comprehensive noninvasive differential diagnostics of these neoplasms.
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Affiliation(s)
- E V Kochurova
- I. M. Sechenov First Moscow State Medical University (Sechenov University), Ministry of Health of the Russian Federation, Moscow, Russia.
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15
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Kochurova EV, Nikolenko VN, Mukhanov AA, Demenchuk PA. [Dental status as a predictive factor in the development of squamous cell carcinoma of the oral mucosa]. STOMATOLOGIIA 2019; 98:34-37. [PMID: 31513146 DOI: 10.17116/stomat20199804134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The aim of this work was to study the influence of components of dental status on the local immunity of the oral cavity; we compared the results of the study of patients with squamous cell carcinoma (SCC) of the oral mucosa and patients without neoplasm. The study involved 136 patients with squamous cell carcinoma of the oral mucosa and 57 patients without neoplasms. In the role of the constituent characteristics of dental status were examined: the use of removable and fixed dentures, dental caries, dental plaque, sharp edges of fullings. Matrix metalloproteinases (MMPs) 2, 8 and 9, as well as their tissue inhibitors 1 and 2 were assessed in oral fluid. The results suggest the influence of all factors on local immune status of the oral cavity as proved by the significant changes in MMPs level. The use of removable dentures resulted in the pronounced decrease of MMPs and should be considered in oral SSC screening and non-invasive diagnostics.
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Affiliation(s)
- E V Kochurova
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | - V N Nikolenko
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | - A A Mukhanov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of Russia, Moscow, Russia
| | - P A Demenchuk
- Burdenko Main Military Clinical Hospital of the Ministry of Defence of Russia, Moscow, Russia
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16
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Baldin AV, Grishina AN, Korolev DO, Kuznetsova EB, Golovastova MO, Kalpinskiy AS, Alekseev BY, Kaprin AD, Zinchenko DV, Savvateeva LV, Varshavsky VA, Zernii EY, Vinarov AZ, Bazhin AV, Philippov PP, Zamyatnin AA. Autoantibody against arrestin-1 as a potential biomarker of renal cell carcinoma. Biochimie 2018; 157:26-37. [PMID: 30389514 DOI: 10.1016/j.biochi.2018.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/25/2018] [Indexed: 12/28/2022]
Abstract
Renal cell carcinoma (RCC) is the second-most common uronephrological cancer. In the absence of specific symptoms, early diagnosis of RCC is challenging. Monitoring of the aberrant expression of tumour-associated antigens (TAAs) and related autoantibody response is considered as a novel approach of RCC diagnostics. The aim of this study was to examine the aberrant expression of arrestin-1 in renal tumours, to investigate the possible epigenetic mechanism underlying arrestin-1 expression, and to assess the frequency of anti-arrestin-1 autoantibody response. Immunohistochemistry was used to assess the presence of arrestin-1 in primary tumours and metastases of 39 patients with RCC and renal oncocytoma. Bisulfite sequencing was employed to analyse the methylation status of the promoter of the SAG gene encoding arrestin-1. Western blot analysis was performed to detect autoantibodies against arrestin-1 in serum samples of 36 RCC and oncocytoma patients. Arrestin-1 was found to be expressed in RCC (58.7% of cases) and renal oncocytoma (90% of cases) cells, while being absent in healthy kidney. The expression of arrestin-1 in RCC metastases was more prominent than in primary tumours. Hypomethylation of the SAG gene promoter is unlikely to be the mechanism for the aberrant expression of arrestin-1. Autoantibodies against arrestin-1 were detected in sera of 75% of RCC patients. Taken together, our findings suggest employment of autoantibody against arrestin-1 as biomarker of RCC.
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Affiliation(s)
- Alexey V Baldin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Alena N Grishina
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Dmitry O Korolev
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Research Centre for Medical Genetics, 115522, Moscow, Russia.
| | - Marina O Golovastova
- Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Alexey S Kalpinskiy
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia
| | - Boris Y Alekseev
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia
| | - Andrey D Kaprin
- P.A. Hertzen Moscow Oncology Research Center, National Medical Research Center of Radiology, 125284, Moscow, Russia.
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.
| | - Lyudmila V Savvateeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Vladimir A Varshavsky
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Evgeni Yu Zernii
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
| | - Andrey Z Vinarov
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
| | - Alexandr V Bazhin
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany.
| | - Pavel P Philippov
- Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia; Department of Cell Signalling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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17
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Cheng JL, Beebe JD, Nepple KG, Zakharia Y, Mullins RF, Flamme-Wiese MJ, Thurtell MJ, Han IC. Autoimmune retinopathy and optic neuropathy associated with enolase-positive renal oncocytoma. Am J Ophthalmol Case Rep 2018; 12:55-60. [PMID: 30229140 PMCID: PMC6140802 DOI: 10.1016/j.ajoc.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/04/2022] Open
Abstract
Purpose To report a case of autoimmune retinopathy and optic neuropathy associated with an enolase-positive renal oncocytoma. Observations A 41-year-old man presented with subacute, painless, bilateral vision loss. On initial examination, visual acuity measured 20/125 OD and 20/1250 OS, and telangiectatic vessels were noted on the optic nerves and in the maculae. Goldmann perimetry showed bilateral, cecocentral scotomas, and electroretinography demonstrated reduced photopic and scotopic signals, concerning for autoimmune retinopathy. Serum testing showed multiple positive anti-optic nerve and anti-retinal antibodies, including to alpha-enolase. Extensive systemic workup was negative except for a large, exophytic, right renal mass. Biopsy was consistent with a benign oncocytoma, and immunohistochemical staining showed diffusely positive alpha-enolase staining. The patient was treated with a five-day course of intravenous methylprednisolone and plasmapheresis with minimal improvement. Surgical excision of the oncocytoma was performed. At 9-months post-operatively, visual acuity had improved to 20/40 OU, with corresponding improvement on visual field and electroretinography testing. Conclusions and importance To our knowledge, this is the first report of autoimmune retinopathy and optic neuropathy associated with a renal oncocytoma. The case highlights the importance of a thorough systemic workup in cases of suspected autoimmune retinopathy and reminds clinicians that even tumors considered benign can have distal effects on other organs.
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Affiliation(s)
- Justine L Cheng
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Johanna D Beebe
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | | | - Yousef Zakharia
- Hematology, Oncology and Bone Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA.,University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Miles J Flamme-Wiese
- Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Matthew J Thurtell
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Ian C Han
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA.,University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
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18
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Abstract
Renal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. While survival rates are high if RCC is diagnosed when still confined to the kidney and treated definitively, there are no specific diagnostic screening tests available and symptoms are rare in early stages of the disease. Management of advanced RCC has changed significantly with the advent of targeted therapies, yet survival is usually increased by months due to acquired resistance to these therapies. DNA methylation, the covalent addition of a methyl group to a cytosine, is essential for normal development and transcriptional regulation, but becomes altered commonly in cancer. These alterations result in broad transcriptional changes, including in tumor suppressor genes. Because DNA methylation is one of the earliest molecular changes in cancer and is both widespread and stable, its role in cancer biology, including RCC, has been extensively studied. In this review, we examine the role of DNA methylation in RCC disease etiology and progression, the preclinical use of DNA methylation alterations as diagnostic, prognostic and predictive biomarkers, and the potential for DNA methylation-directed therapies.
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Affiliation(s)
- Brittany N Lasseigne
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806-2908, USA.
| | - James D Brooks
- Department of Urology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA, 94305-5118, USA
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19
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Michels J, Becker N, Suciu S, Kaiser I, Benner A, Kosaloglu-Yalcin Z, Agoussi S, Halama N, Pawlita M, Waterboer T, Eichmüller SB, Jäger D, Eggermont AMM, Zörnig I. Multiplex bead-based measurement of humoral immune responses against tumor-associated antigens in stage II melanoma patients of the EORTC18961 trial. Oncoimmunology 2018; 7:e1428157. [PMID: 29872552 PMCID: PMC5980408 DOI: 10.1080/2162402x.2018.1428157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/07/2018] [Accepted: 01/09/2018] [Indexed: 12/25/2022] Open
Abstract
Purpose: Determine the prognostic and predictive significance of tumor associated antigen (TAA)-specific serum antibodies in melanoma patients of a large adjuvant vaccination phase III trial. Patients and methods: Serum IgG antibodies were measured against a panel of 43 antigens by a bead-based multiplex assay in 970 stage II melanoma patients of the EORTC18961 trial, evaluating adjuvant ganglioside GM2-KLH/QS-21 vaccination versus observation. Primary end point was relapse-free survival (RFS). Patients' sera at baseline, after 12 and 48 weeks of study treatment and at the last available time point (at recurrence/remission) were evaluated. Results: Prognostic clinical variables are gender, surgical confirmation of lymph node-negative status, Breslow thickness and ulceration of the primary. Prognostic spontaneous antibody responses were associated with a significant dismal (GM2, Rhod_E2, SSX2) or good prognosis (CyclinB1, SCYE1v1) for RFS, distant metastasis-free (DMFS) or overall survival (OS). Predictive spontaneous antibody responses based on significant interaction with treatment were RhodN p = 0.02, Rab38 p = 0.04 for RFS, RhodE2 p = 0.006, Recoverin p = 0.04 for DMFS and RhodE2 p = 0.003; Recoverin p = 0.04, NA17.A p = 0.04, for OS respectively. The subgroups of patients according to antibody responses for RFS were determined for RhodN sero-negative (n = 849, HR = 1.07, p = 0.6); RhodN sero-positive (n = 121,HR = 0.42, p = 0.01) and Rab38 sero-negative (n = 682, HR = 1.12, p = 0.42), Rab38 sero-positive (n = 288, HR = 0.65, p = 0.04) patients respectively. Conclusion: We identified prognostic serum antibody responses against TAA in stage II melanoma patients. A set of antibody responses correlated with a beneficial outcome for GM2 vaccination.
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Affiliation(s)
- Judith Michels
- Department of Medical Oncology, Gustave Roussy Comprehensive Cancer Center, Villejuif/Paris-Sud, France.,Université Paris-Sud, Kremlin Bicêtre, Paris, France
| | - Natalia Becker
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Suciu
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | - Iris Kaiser
- Department of Medical Oncology, National Center for Tumor Diseases, Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zeynep Kosaloglu-Yalcin
- Clincial Cooperation Unit "Applied Tumor Immunity", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandrine Agoussi
- INSERM U981, Gustave Roussy Comprehensive Cancer Center, Villejuif/Paris-Sud, France
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases, Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B Eichmüller
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk Jäger
- Department of Medical Oncology, National Center for Tumor Diseases, Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany.,Clincial Cooperation Unit "Applied Tumor Immunity", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander M M Eggermont
- Department of Medical Oncology, Gustave Roussy Comprehensive Cancer Center, Villejuif/Paris-Sud, France.,Université Paris-Sud, Kremlin Bicêtre, Paris, France
| | - Inka Zörnig
- Department of Medical Oncology, National Center for Tumor Diseases, Internal Medicine VI, Heidelberg University Hospital, Heidelberg, Germany
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20
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Joosten SC, Deckers IA, Aarts MJ, Hoeben A, van Roermund JG, Smits KM, Melotte V, van Engeland M, Tjan-Heijnen VC. Prognostic DNA methylation markers for renal cell carcinoma: a systematic review. Epigenomics 2017; 9:1243-1257. [PMID: 28803494 DOI: 10.2217/epi-2017-0040] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM Despite numerous published prognostic methylation markers for renal cell carcinoma (RCC), none of these have yet changed patient management. Our aim is to systematically review and evaluate the literature on prognostic DNA methylation markers for RCC. MATERIALS & METHODS We conducted an exhaustive search of PubMed, EMBASE and MEDLINE up to April 2017 and identified 49 publications. Studies were reviewed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, assessed for their reporting quality using the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) criteria, and were graded to determine the level of evidence (LOE) for each biomarker. RESULTS We identified promoter methylation of BNC1, SCUBE3, GATA5, SFRP1, GREM1, RASSF1A, PCDH8, LAD1 and NEFH as promising prognostic markers. Extensive methodological heterogeneity across the included studies was observed, which hampers comparability and reproducibility of results, providing a possible explanation why these biomarkers do not reach the clinic. CONCLUSION Potential prognostic methylation markers for RCC have been identified, but they require further validation in prospective studies to determine their true clinical value.
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Affiliation(s)
- Sophie C Joosten
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ivette Ag Deckers
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Maureen J Aarts
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Ann Hoeben
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Joep G van Roermund
- Department of Urology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M Smits
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands.,Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Veerle Melotte
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C Tjan-Heijnen
- Division of Medical Oncology, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
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Golovastova MO, Korolev DO, Tsoy LV, Varshavsky VA, Xu WH, Vinarov AZ, Zernii EY, Philippov PP, Zamyatnin AA. Biomarkers of Renal Tumors: the Current State and Clinical Perspectives. Curr Urol Rep 2017; 18:3. [PMID: 28110463 DOI: 10.1007/s11934-017-0655-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Renal cell carcinoma (RCC) ranks the first death rate among the urogenital tumors, whereas its incidence follows the incidences of prostate and bladder cancer. The diagnosis of RCC at early stages allows immediately undertaking appropriate treatment, which significantly increases patients' survival rate. Early and accurate diagnosis avoids inadequate treatment, provides the disease progression forecast, and permits to apply more efficient therapy. Unfortunately, the small renal tumors are usually asymptomatic resulting in the late diagnosis and, therefore, low efficacy of treatment. Thus, sensible and preventive biomarkers are essential for early RCC detection and monitoring of its progression. So far, many attempts were performed aimed at recognizing novel informative kidney tumor biomarkers applicable for early detection of the disease and possessing prognostic and predictive capabilities. This review summarizes recent advances in renal tumor biomarkers recognition, their diagnostic and prognostic values, and clinical feasibility.
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Affiliation(s)
- Marina O Golovastova
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Dmitry O Korolev
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Larisa V Tsoy
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Vladimir A Varshavsky
- Anatomic Pathology Department, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Wan-Hai Xu
- Department of Urology, The Fourth Hospital of Harbin Medical University, Harbin, China
| | - Andrey Z Vinarov
- Institute of Uronephrology and Human Reproductive Health, Sechenov First Moscow State Medical University, 119991, Moscow, Russia
| | - Evgeni Yu Zernii
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Pavel P Philippov
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Andrey A Zamyatnin
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia.
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