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Sultanov R, Mulyukina A, Zubkova O, Fedoseeva A, Bogomazova A, Klimina K, Larin A, Zatsepin T, Prikazchikova T, Lukina M, Bogomiakova M, Sharova E, Generozov E, Lagarkova M, Arapidi G. TP63-TRIM29 axis regulates enhancer methylation and chromosomal instability in prostate cancer. Epigenetics Chromatin 2024; 17:6. [PMID: 38481282 PMCID: PMC10938740 DOI: 10.1186/s13072-024-00529-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Prostate adenocarcinoma (PRAD) is the second leading cause of cancer-related deaths in men. High variability in DNA methylation and a high rate of large genomic rearrangements are often observed in PRAD. RESULTS To investigate the reasons for such high variance, we integrated DNA methylation, RNA-seq, and copy number alterations datasets from The Cancer Genome Atlas (TCGA), focusing on PRAD, and employed weighted gene co-expression network analysis (WGCNA). Our results show that only single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators and are downregulated in PRAD. We discovered that TP63 regulates the level of enhancer methylation in prostate basal epithelial cells. TRIM29 forms a complex with TP63 and together regulates the expression of genes specific to the prostate basal epithelium. In addition, TRIM29 binds DNA repair proteins and prevents the formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. CONCLUSION Our study demonstrates that TRIM29 and TP63 are important regulators in maintaining the identity of the basal epithelium under physiological conditions. Furthermore, we uncover the role of TRIM29 in PRAD development.
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Affiliation(s)
- R Sultanov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.
| | - A Mulyukina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - O Zubkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - A Fedoseeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - A Bogomazova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - K Klimina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - A Larin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - T Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - T Prikazchikova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - M Lukina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - M Bogomiakova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - E Sharova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - E Generozov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - M Lagarkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - G Arapidi
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
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Russo V, Tamburrino L, Morselli S, Sani C, Baldi E, Sebastianelli A, Raspollini MR, Mongia A, Carradori V, Lallo E, Munnia A, Bisanzi S, Marchiani S, Visioli C, Rapi S, Serni S, Zappa M, Carozzi F, Peluso M. Hyperglycemia and microRNAs in prostate cancer. Prostate Cancer Prostatic Dis 2024:10.1038/s41391-024-00809-z. [PMID: 38402304 DOI: 10.1038/s41391-024-00809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Hyperglycemia can promote the development of prostate cancer (PCa). Differential expression levels of miRNAs between PCa patients and controls were also reported. Therefore, we examined the relationship between hyperglycemia and miRNA levels in PCa. METHODS Relative expression of urinary miR-574-3p, miR-375, miR-205-5p, miR-200b-3p, miR-187-3p, miR-182-5p, and miR-100-5p were investigated in 105 PCa patients and 138 noncancer controls by Real-Time quantitative PCR. Fasting plasma glucose measurements were retrieved from clinical records. The differential miRNA expressions among groups were compared using non-parametric tests. Correlations with glucose and prostate-specific antigen (PSA) were tested using Pearson correlation coefficient. RESULTS When we analyzed miRNA expression according to glycemic state, significant down-regulations were found for miR-200b-3p, miR-187-3p, miR-182-5p, and miR-100-5p in noncancer controls with high glucose. The lowest down-regulations were observed for miR-187-3p, miR-182-5p, and miR-100-5p. Subsequently, when hyperglycemia was considered in PCa, significant dysregulations of selected miRNAs were found in hyperglycemic PCa patients than in controls with high glucose. In particular, miR-375 and miR-182-5p showed a 3-FC in hyperglycemic PCa patients than controls who left hyperglycemia untreated. Conversely, only a down-regulation of miR-574-3p was observed in PCa patients regardless of glycemic status and only modest down-regulation of miR-574-3p, miR-200b-3p, miR-187-3p and miR-182-5p were found in normoglycemic PCa patients. Next, significant correlations between miRNAs and glucose (miR-200b-3p, miR-100-5p) and PSA (miR-205-5p and miR-187-3p) were detected in controls. Similarly, miR-205-5p and miR-187-3p were correlated with glucose in PCa patients, while miR-574-3p and miR-375 showed inverse relationships. CONCLUSIONS miRNA dysregulations can occur in hyperglycemic PCa patients as compared to noncancer controls who left hyperglycemia untreated. Hyperglycemia can consistently promote the expression of miR-375 and miR-182-5p. Uncontrolled hyperglycemic state could contribute to the creation of a suitable microenvironment for later PCa development by promoting gene expression.
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Affiliation(s)
- Valentina Russo
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Lara Tamburrino
- Andrology, Women's Endocrinology and Gender Incongruence Unit, Center for Prevention, Diagnosis and Treatment of Infertility, Careggi University Hospital, 50139, Florence, Italy
| | - Simone Morselli
- Department of Urology, Hesperia Hospital, 41125, Modena, Italy
- Centro Urologico Europeo (CUrE), 41125, Modena, Italy
- Unit of Urological Robotic Surgery and Renal Transplantation, Careggi University Hospital, 50139, Florence, Italy
| | - Cristina Sani
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Elisabetta Baldi
- Andrology, Women's Endocrinology and Gender Incongruence Unit, Center for Prevention, Diagnosis and Treatment of Infertility, Careggi University Hospital, 50139, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, 50139, Florence, Italy
| | - Arcangelo Sebastianelli
- Unit of Urological Robotic Surgery and Renal Transplantation, Careggi University Hospital, 50139, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, 50139, Florence, Italy
| | - Maria Rosaria Raspollini
- Department of Experimental and Clinical Medicine, University of Florence, 50139, Florence, Italy
- Department of Histopathology and Molecular Diagnostics, Careggi University Hospital, 50139, Florence, Italy
| | - Alessandra Mongia
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Valentina Carradori
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Eleonora Lallo
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Armelle Munnia
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Simonetta Bisanzi
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Sara Marchiani
- Andrology, Women's Endocrinology and Gender Incongruence Unit, Center for Prevention, Diagnosis and Treatment of Infertility, Careggi University Hospital, 50139, Florence, Italy
- Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, 50139, Florence, Italy
| | - Carmen Visioli
- Division of Epidemiology and Clinical Governance, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Stefano Rapi
- Clinical Chemistry Laboratory Unit, S. Luca Hospital, USL Toscana Nord Ovest, 55100, Lucca, Italy
| | - Sergio Serni
- Unit of Urological Robotic Surgery and Renal Transplantation, Careggi University Hospital, 50139, Florence, Italy
- Department of Experimental and Clinical Medicine, University of Florence, 50139, Florence, Italy
| | - Marco Zappa
- Retired, formerly at Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Francesca Carozzi
- Retired, formerly at Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Marco Peluso
- Regional Laboratory of Cancer Prevention, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy.
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Gomari MM, Arab SS, Balalaie S, Ramezanpour S, Hosseini A, Dokholyan NV, Tarighi P. Rational peptide design for targeting cancer cell invasion. Proteins 2024; 92:76-95. [PMID: 37646459 DOI: 10.1002/prot.26580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
Cell invasion is an important process in cancer progression and recurrence. Invasion and implantation of cancer cells from their original place to other tissues, by disabling vital organs, challenges the treatment of cancer patients. Given the importance of the matter, many molecular treatments have been developed to inhibit cancer cell invasion. Because of their low production cost and ease of production, peptides are valuable therapeutic molecules for inhibiting cancer cell invasion. In recent years, advances in the field of computational biology have facilitated the design of anti-cancer peptides. In our investigation, using computational biology approaches such as evolutionary analysis, residue scanning, protein-peptide interaction analysis, molecular dynamics, and free energy analysis, our team designed a peptide library with about 100 000 candidates based on A6 (acetyl-KPSSPPEE-amino) sequence which is an anti-invasion peptide. During computational studies, two of the designed peptides that give the highest scores and showed the greatest sequence similarity to A6 were entered into the experimental analysis workflow for further analysis. In experimental analysis steps, the anti-metastatic potency and other therapeutic effects of designed peptides were evaluated using MTT assay, RT-qPCR, zymography analysis, and invasion assay. Our study disclosed that the IK1 (acetyl-RPSFPPEE-amino) peptide, like A6, has great potency to inhibit the invasion of cancer cells.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Balalaie
- Peptide Chemistry Research Institute, K. N. Toosi University of Technology, Tehran, Iran
| | - Sorour Ramezanpour
- Department of Chemistry, K. N. Toosi University of Technology, Tehran, Iran
| | - Arshad Hosseini
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
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Buhigas C, Warren AY, Leung WK, Whitaker HC, Luxton HJ, Hawkins S, Kay J, Butler A, Xu Y, Woodcock DJ, Merson S, Frame FM, Sahli A, Abascal F, Martincorena I, Bova GS, Foster CS, Campbell P, Maitland NJ, Neal DE, Massie CE, Lynch AG, Eeles RA, Cooper CS, Wedge DC, Brewer DS. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Mol Cancer 2022; 21:183. [PMID: 36131292 PMCID: PMC9494848 DOI: 10.1186/s12943-022-01644-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/17/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Up to 80% of cases of prostate cancer present with multifocal independent tumour lesions leading to the concept of a field effect present in the normal prostate predisposing to cancer development. In the present study we applied Whole Genome DNA Sequencing (WGS) to a group of morphologically normal tissue (n = 51), including benign prostatic hyperplasia (BPH) and non-BPH samples, from men with and men without prostate cancer. We assess whether the observed genetic changes in morphologically normal tissue are linked to the development of cancer in the prostate. RESULTS Single nucleotide variants (P = 7.0 × 10-03, Wilcoxon rank sum test) and small insertions and deletions (indels, P = 8.7 × 10-06) were significantly higher in morphologically normal samples, including BPH, from men with prostate cancer compared to those without. The presence of subclonal expansions under selective pressure, supported by a high level of mutations, were significantly associated with samples from men with prostate cancer (P = 0.035, Fisher exact test). The clonal cell fraction of normal clones was always higher than the proportion of the prostate estimated as epithelial (P = 5.94 × 10-05, paired Wilcoxon signed rank test) which, along with analysis of primary fibroblasts prepared from BPH specimens, suggests a stromal origin. Constructed phylogenies revealed lineages associated with benign tissue that were completely distinct from adjacent tumour clones, but a common lineage between BPH and non-BPH morphologically normal tissues was often observed. Compared to tumours, normal samples have significantly less single nucleotide variants (P = 3.72 × 10-09, paired Wilcoxon signed rank test), have very few rearrangements and a complete lack of copy number alterations. CONCLUSIONS Cells within regions of morphologically normal tissue (both BPH and non-BPH) can expand under selective pressure by mechanisms that are distinct from those occurring in adjacent cancer, but that are allied to the presence of cancer. Expansions, which are probably stromal in origin, are characterised by lack of recurrent driver mutations, by almost complete absence of structural variants/copy number alterations, and mutational processes similar to malignant tissue. Our findings have implications for treatment (focal therapy) and early detection approaches.
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Affiliation(s)
- Claudia Buhigas
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Wing-Kit Leung
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - Hayley C Whitaker
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, Division of Surgery and Interventional Sciences University College London, London, W1W 7TS, UK
| | - Hayley J Luxton
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, Division of Surgery and Interventional Sciences University College London, London, W1W 7TS, UK
| | - Steve Hawkins
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - Jonathan Kay
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, Division of Surgery and Interventional Sciences University College London, London, W1W 7TS, UK
| | - Adam Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Yaobo Xu
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Sue Merson
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, Heslington, YO10 5DD, North Yorkshire, UK
| | - Atef Sahli
- Oxford Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - G Steven Bova
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33014, Tampere, FI, Finland
| | | | - Peter Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, Heslington, YO10 5DD, North Yorkshire, UK
| | - David E Neal
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - Charlie E Massie
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- School of Medicine/School of Mathematics and Statistics, University of St Andrews, St Andrews, KY16 9AJ, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, SM2 5PT, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - David C Wedge
- Oxford Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- Earlham Institute, Norwich, NR4 7UZ, UK.
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Qie Y, Zhou D, Wu Z, Liu S, Shen C, Hu H, Zhang C, Xu Y. Low-dose hexavalent chromium(VI) exposure promotes prostate cancer cell proliferation by activating MAGEB2-AR signal pathway. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113724. [PMID: 35660381 DOI: 10.1016/j.ecoenv.2022.113724] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/15/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Hexavalent chromium [Cr(VI)], one common environmental contaminant, has long been recognized as a carcinogen associated with several malignancies, such as lung cancer, but little information was available about the effects of its low-dose environmental exposure in prostate cancer. Our previous study has shown that low-dose Cr(VI) exposure could promote prostate cancer(PCa) cell growth in vitro and in vivo. In the present study, we furthermore found that low-dose Cr(VI) exposure could induce DNA demethylation in PCa cells. Based on our transcriptome sequencing data and DNA methylation database, we further identified MAGEB2 as a potential effector target that contributed to tumor-promoting effect of low-dose Cr(VI) exposure in PCa. In addition, we demonstrated that MAGEB2 was upregulated in PCa and its knockdown restrained PCa cell proliferation and tumor growth in vitro and in vivo. Moreover, Co-IP and point mutation experiments confirmed that MAGEB2 could bind to the NH2-terminal NTD domain of AR through the F-box in the MAGE homology domain, and then activated AR through up-regulating its downstream targets PSA and NX3.1. Together, low-dose Cr(VI) exposure can induce DNA demethylation in prostate cancer cells, and promote cell proliferation via activating MAGEB2-AR signaling pathway. Thus, inhibition of MAGEB2-AR signaling is a novel and promising strategy to reverse low-dose Cr(VI) exposure-induced prostate tumor progression, also as effective adjuvant therapy for AR signaling-dependent PCa.
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Affiliation(s)
- Yunkai Qie
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China; CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Diansheng Zhou
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Zhouliang Wu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Shenglai Liu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Chong Shen
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Hailong Hu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Changwen Zhang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China.
| | - Yong Xu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China.
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Ye C, Wang H, Li Z, Xia C, Yuan S, Yan R, Yang X, Ma T, Wen X, Yang D. Comprehensive data analysis of genomics, epigenomics, and transcriptomics to identify specific biomolecular markers for prostate adenocarcinoma. Transl Androl Urol 2021; 10:3030-3045. [PMID: 34430406 PMCID: PMC8350225 DOI: 10.21037/tau-21-576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background Multiomics data analysis based on high-throughput sequencing technology has become a hotspot in tumor investigation. The present study aimed to explore prognostic biomarkers via investigating DNA copy number variation (CNV) and methylation variation (MET) data in prostate cancer. Methods We obtained the messenger RNA (mRNA) expression, CNV, and methylated data of prostate adenocarcinoma (PRAD) samples via The Cancer Genome Atlas (TCGA)-PRAD cohort. We calculated and assessed the associations between CNV and RNA sequencing (RNA-seq), and between MET and RNA-seq via Pearson correlation coefficients. We then used the "iCluster" package to perform multigroup cluster analysis with CNVcor gene CNV data, METcor gene methylation data, and CNVcor and METcor gene mRNA data. The univariate Cox analysis was used to screen significant hub genes, and multivariate Cox analysis was used to construct risk a model. The nomogram was constructed based on "rms" package, and the immune infiltrating patterns were compared between high- and low-risk groups. Results A total of 477 PRAD samples with complete CNV, methylation, mRNA, and matched clinical information were included in our study. A list of 10,073 CNVcor genes and 9841 METcor genes were confirmed with a significance level of P<0.01. We found that CNVcor is more likely to appear on chromosome (chr)8, chr17, and chr10, while METcor is more likely to appear on chr1, chr19, and chr17. Based on the core genes, we finally classified the samples into 4 subtypes, incorporating iC1 (iCluster) (92 samples), iC2 (79 samples), iC3 (165 samples), and iC4 (141 samples). Furthermore, we constructed the prognostic model for PRAD based on the 5 genes (IER3, AOX1, PRKCDBP, UBD, and FBLN5). Nomograms incorporating risk score and other clinical variables were further constructed, and these nomograms exhibited superior predictive ability. We further compared the differential immune infiltrating patterns in 2 risk groups and found significantly low levels of infiltrating cluster of differentiation (CD)8+ T cells in high-risk samples. Conclusions Our study integrated the multi-omics data to elucidate the molecular features of PRAD and pivotal genes for predicting prognosis.
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Affiliation(s)
- Chunwei Ye
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haifeng Wang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhipeng Li
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chengxing Xia
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shunhui Yuan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruping Yan
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaofang Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Tao Ma
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xingqiao Wen
- Department of Urology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Delin Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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7
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Maitland NJ. Resistance to Antiandrogens in Prostate Cancer: Is It Inevitable, Intrinsic or Induced? Cancers (Basel) 2021; 13:327. [PMID: 33477370 PMCID: PMC7829888 DOI: 10.3390/cancers13020327] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/20/2022] Open
Abstract
Increasingly sophisticated therapies for chemical castration dominate first-line treatments for locally advanced prostate cancer. However, androgen deprivation therapy (ADT) offers little prospect of a cure, as resistant tumors emerge rather rapidly, normally within 30 months. Cells have multiple mechanisms of resistance to even the most sophisticated drug regimes, and both tumor cell heterogeneity in prostate cancer and the multiple salvage pathways result in castration-resistant disease related genetically to the original hormone-naive cancer. The timing and mechanisms of cell death after ADT for prostate cancer are not well understood, and off-target effects after long-term ADT due to functional extra-prostatic expression of the androgen receptor protein are now increasingly being recorded. Our knowledge of how these widely used treatments fail at a biological level in patients is deficient. In this review, I will discuss whether there are pre-existing drug-resistant cells in a tumor mass, or whether resistance is induced/selected by the ADT. Equally, what is the cell of origin of this resistance, and does it differ from the treatment-naïve tumor cells by differentiation or dedifferentiation? Conflicting evidence also emerges from studies in the range of biological systems and species employed to answer this key question. It is only by improving our understanding of this aspect of treatment and not simply devising another new means of androgen inhibition that we can improve patient outcomes.
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Affiliation(s)
- Norman J Maitland
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
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Paczkowski M, Kretzschmar WW, Markelc B, Liu SK, Kunz-Schughart LA, Harris AL, Partridge M, Byrne HM, Kannan P. Reciprocal interactions between tumour cell populations enhance growth and reduce radiation sensitivity in prostate cancer. Commun Biol 2021; 4:6. [PMID: 33398023 PMCID: PMC7782740 DOI: 10.1038/s42003-020-01529-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/24/2020] [Indexed: 01/29/2023] Open
Abstract
Intratumoural heterogeneity (ITH) contributes to local recurrence following radiotherapy in prostate cancer. Recent studies also show that ecological interactions between heterogeneous tumour cell populations can lead to resistance in chemotherapy. Here, we evaluated whether interactions between heterogenous populations could impact growth and response to radiotherapy in prostate cancer. Using mixed 3D cultures of parental and radioresistant populations from two prostate cancer cell lines and a predator-prey mathematical model to investigate various types of ecological interactions, we show that reciprocal interactions between heterogeneous populations enhance overall growth and reduce radiation sensitivity. The type of interaction influences the time of regrowth after radiation, and, at the population level, alters the survival and cell cycle of each population without eliminating either one. These interactions can arise from oxygen constraints and from cellular cross-talk that alter the tumour microenvironment. These findings suggest that ecological-type interactions are important in radiation response and could be targeted to reduce local recurrence.
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Affiliation(s)
| | - Warren W Kretzschmar
- School of Engineering Sciences in Chemistry Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine (HERM), Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine (HERM), Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Bostjan Markelc
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Stanley K Liu
- Sunnybrook Research Institute and Departments of Medical Biophysics and Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Leoni A Kunz-Schughart
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum, Dresden, Rossendorf, Germany
- National Center for Tumor Diseases (NCT), Partner Site, Dresden, Germany
| | - Adrian L Harris
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mike Partridge
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Helen M Byrne
- Mathematical Institute, University of Oxford, Oxford, UK.
| | - Pavitra Kannan
- CRUK and MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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Cheng S, Xie W, Miao Y, Guo J, Wang J, Li C, Zhang Y. Identification of key genes in invasive clinically non-functioning pituitary adenoma by integrating analysis of DNA methylation and mRNA expression profiles. J Transl Med 2019; 17:407. [PMID: 31796052 PMCID: PMC6892283 DOI: 10.1186/s12967-019-02148-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tumor surrounding the internal carotid artery or invading to the cavernous sinus is an important characteristic of invasive pituitary adenoma, and a pivotal factor of tumor residue and regrowth. Without specific changes in serum hormone related to the adenohypophyseal cell of origin, clinically non-functioning pituitary adenoma is more likely to be diagnosed at invasive stages compared with functioning pituitary adenoma. The underlying mechanism of tumor invasion remains unknown. In this study, we aimed to identify key genes in tumor invasion by integrating analyses of DNA methylation and gene expression profiles. METHOD Genome-wide DNA methylation and mRNA microarray analysis were performed for tumor samples from 68 patients at the Beijing Tiantan Hospital. Differentially expressed genes and methylated probes were identified based on an invasive vs non-invasive grouping. Differentially methylated probes in the promoter region of targeted genes were assessed. Pearson correlation analysis was used to identify genes with a strong association between DNA methylation status and expression levels. Pyrosequencing and RT-PCR were used to validate the methylation status and expression levels of candidate genes, respectively. RESULTS A total of 8842 differentially methylated probes, located on 4582 genes, and 661 differentially expressed genes were identified. Both promoter methylation and expression alterations were observed for 115 genes with 58 genes showing a negative correlation between DNA methylation status and expression level. Nineteen genes that exhibited notably negative correlations between DNA methylation and gene expression levels, are involved in various gene ontologies and pathways, or played an important role in different diseases, were regarded as candidate genes. We found an increased methylation with a decreased expression of PHYHD1, LTBR, C22orf42, PRR5, ANKDD1A, RAB13, CAMKV, KIFC3, WNT4 and STAT6, and a decreased methylation with an increased expression of MYBPHL. The methylation status and expression levels of these genes were validated by pyrosequencing and RT-PCR. CONCLUSIONS The DNA methylation and expression levels of PHYHD1, LTBR, MYBPHL, C22orf42, PRR5, ANKDD1A, RAB13, CAMKV, KIFC3, WNT4 and STAT6 are associated with tumor invasion, and these genes may become the potential genes for targeted therapy.
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Affiliation(s)
- Sen Cheng
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070 China
| | - Weiyan Xie
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070 China
| | - Yazhou Miao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070 China
| | - Jing Guo
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070 China
| | - Jichao Wang
- People’s Hospital of Xin Jiang Uygur Autonomous Region, Urumqi, 830001 China
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing Institute for Brain Disorders Brain Tumor Center, China National Clinical Research Center for Neurological Diseases, Key Laboratory of Central Nervous System Injury Research, Beijing, 100070 China
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital Affiliated to Capital Medical University, Beijing Institute for Brain Disorders Brain Tumor Center, China National Clinical Research Center for Neurological Diseases, Key Laboratory of Central Nervous System Injury Research, Beijing, 100070 China
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Maitland NJ, Frame FM, Rane JK, Erb HH, Packer JR, Archer LK, Pellacani D. Resolution of Cellular Heterogeneity in Human Prostate Cancers: Implications for Diagnosis and Treatment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1164:207-224. [PMID: 31576551 DOI: 10.1007/978-3-030-22254-3_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Prostate cancers have a justified reputation as one of the most heterogeneous human tumours. Indeed, there are some who consider that advanced and castration-resistant prostate cancers are incurable, as a direct result of this heterogeneity. However, tumour heterogeneity can be defined in different ways. To a clinician, prostate cancer is a number of different diseases, the treatments for which remain equally heterogeneous and uncertain. To the pathologist, the histopathological appearances of the tumours are notoriously heterogeneous. Indeed, the genius of Donald Gleason in the 1960s was to devise a classification system designed to take into account the heterogeneity of the tumours both individually and in the whole prostate context. To the cell biologist, a prostate tumour consists of multiple epithelial cell types, inter-mingled with various fibroblasts, neuroendocrine cells, endothelial cells, macrophages and lymphocytes, all of which interact to influence treatment responses in a patient-specific manner. Finally, genetic analyses of prostate cancers have been compromised by the variable gene rearrangements and paucity of activating mutations observed, even in large numbers of patient tumours with consistent clinical diagnoses and/or outcomes. Research into familial susceptibility has even generated the least tractable outcome of such studies: the genetic loci are of low penetrance and are of course heterogeneous. By fractionating the tumour (and patient-matched non-malignant tissues) heterogeneity can be resolved, revealing homogeneous markers of patient outcomes.
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Affiliation(s)
- Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, York, UK.
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, York, UK
| | - Jayant K Rane
- Cancer Research Unit, Department of Biology, University of York, York, UK
| | - Holger H Erb
- Cancer Research Unit, Department of Biology, University of York, York, UK
| | - John R Packer
- Cancer Research Unit, Department of Biology, University of York, York, UK
| | - Leanne K Archer
- Cancer Research Unit, Department of Biology, University of York, York, UK
| | - Davide Pellacani
- Cancer Research Unit, Department of Biology, University of York, York, UK.,Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
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11
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Frame FM, Maitland NJ. Epigenetic Control of Gene Expression in the Normal and Malignant Human Prostate: A Rapid Response Which Promotes Therapeutic Resistance. Int J Mol Sci 2019; 20:E2437. [PMID: 31108832 PMCID: PMC6566891 DOI: 10.3390/ijms20102437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
A successful prostate cancer must be capable of changing its phenotype in response to a variety of microenvironmental influences, such as adaptation to treatment or successful proliferation at a particular metastatic site. New cell phenotypes emerge by selection from the large, genotypically heterogeneous pool of candidate cells present within any tumor mass, including a distinct stem cell-like population. In such a multicellular model of human prostate cancer, flexible responses are primarily governed not only by de novo mutations but appear to be dominated by a combination of epigenetic controls, whose application results in treatment resistance and tumor relapse. Detailed studies of these individual cell populations have resulted in an epigenetic model for epithelial cell differentiation, which is also instructive in explaining the reported high and inevitable relapse rates of human prostate cancers to a multitude of treatment types.
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Affiliation(s)
- Fiona M Frame
- The Cancer Research Unit, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - Norman J Maitland
- The Cancer Research Unit, Department of Biology, University of York, Heslington, York YO10 5DD, UK.
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