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Yu J, Gong Y, Xu Z, Chen L, Li S, Cui Y. Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling. PeerJ 2024; 12:e17629. [PMID: 38938617 PMCID: PMC11210462 DOI: 10.7717/peerj.17629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
While the significance of immunogenic cell death (ICD) in oncology is acknowledged, its specific impact on colorectal carcinoma remains underexplored. In this study, we delved into the role of ICD in colorectal carcinoma, a topic not yet comprehensively explored. A novel ICD quantification system was developed to forecast patient outcomes and the effectiveness of immunotherapy. Utilizing single-cell sequencing, we constructed an ICD score within the tumor immune microenvironment (TIME) and examined immunogenic cell death related genes (ICDRGs). Using data from TCGA and GEO, we discovered two separate molecular subcategories within 1,184 patients diagnosed with colon adenocarcinoma/rectum adenocarcinoma (COADREAD). The ICD score was established by principal component analysis (PCA), which classified patients into groups with low and high ICD scores. Further validation in three independent cohorts confirmed the model's accuracy in predicting immunotherapy success. Patients with higher ICD scores exhibited a "hot" immune phenotype and showed increased responsiveness to immunotherapy. Key genes in the model, such as AKAP12, CALB2, CYR61, and MEIS2, were found to enhance COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offered a new avenue for anti-tumor strategies by targeting ICD, marking advances in colorectal carcinoma treatment.
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Affiliation(s)
- Jinglu Yu
- PuDong Traditional Chinese Medicine Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China, Shanghai, Pudong, China
| | - Yabin Gong
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Zhenye Xu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Lei Chen
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui District, China
| | - Shuang Li
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yongkang Cui
- Department of Gastroenterology, Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Chen JP, Diekmann C, Wu H, Chen C, Della Chiara G, Berrino E, Georgiadis KL, Bouwman BAM, Virdi M, Harbers L, Bellomo SE, Marchiò C, Bienko M, Crosetto N. scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat Commun 2024; 15:1768. [PMID: 38409079 PMCID: PMC10897160 DOI: 10.1038/s41467-024-45972-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.
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Affiliation(s)
- Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, PR China
- School of Life Sciences, Peking University, Beijing, PR China
| | - Chong Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Konstantinos L Georgiadis
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Britta A M Bouwman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Mohit Virdi
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
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3
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Chen W, Wang Y, Gu H, Zhang Y, Chen C, Yu T, Chen T. Molecular characteristics, clinical significance, and immune landscape of extracellular matrix remodeling-associated genes in colorectal cancer. Front Oncol 2023; 13:1109181. [PMID: 37621680 PMCID: PMC10446763 DOI: 10.3389/fonc.2023.1109181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Background Extracellular matrix (ECM) remodeling is one of the hallmark events in cancer and has been shown to be closely related to tumor immunity. Immunotherapy has evolved as an important tool to treat various cancers and improve patient prognosis. The positive response to immunotherapy relies on the unique interaction between cancer and the tumor microenvironment (TME). However, the relationship between ECM remodeling and clinical outcomes, immune cell infiltration, and immunotherapy in colorectal cancer (CRC) remains unknown. Methods We systematically evaluated 69 ECM remodeling-associated genes (EAGs) and comprehensively identified interactions between ECM remodeling and prognosis and the immune microenvironment in CRC patients. The EAG_score was used to quantify the subtype of ECM remodeling in patients. We then assessed their value in predicting prognosis and responding to treatment in CRC. Results After elaborating the molecular characteristics of ECM remodeling-related genes in CRC patients, a model consisting of two ECM remodeling-related genes (MEIS2, SLC2A3) was developed for predicting the prognosis of CRC patients, Receiver Operating Characteristic (ROC) and Kaplan-Meier (K-M) analysis verified its reliable predictive ability. Furthermore, we created a highly reliable nomogram to enhance the clinical feasibility of the EAG_score. Significantly differences in TME and immune function, such as macrophages and CD8+ T cells, were observed between high- and low-risk CRC patients. In addition, drug sensitivity is also strongly related to EAG_score. Conclusion Overall, we developed a prognostic model associated with ECM remodeling, provided meaningful clinical implications for immunotherapy, and facilitated individualized treatment for CRC patients. Further studies are needed to reveal the underlying mechanisms of ECM remodeling in CRC.
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Affiliation(s)
- Wenlong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiwen Wang
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haitao Gu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cong Chen
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tingting Yu
- Department of Medical Genetics, School of Basic Medical Science, Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
| | - Tao Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Han D, Li X, Cheng Y. Transcription Factor ELF1 Modulates Cisplatin Sensitivity in Prostate Cancer by Targeting MEIS Homeobox 2. Chem Res Toxicol 2023; 36:360-368. [PMID: 36763086 DOI: 10.1021/acs.chemrestox.2c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
As a widely used first-line agent for prostate cancer treatment, cisplatin is facing drug resistance which has resulted in chemotherapy failure in many prostate cancer patients, while the related molecular mechanisms remain unclear. In this study, we discovered that MEIS homeobox 2 (MEIS2) was lowly expressed in prostate cancer tissues by bioinformatics analysis, which had a close connection with the T stage and N stage of the tumor. Cell function experiments demonstrated that MEIS2 overexpression was capable of significantly suppressing proliferation of tumor cells, arresting prostate cancer cells in G0/G1 phase, and promoting DNA damage, thereby enhancing the sensitivity of prostate cancer to cisplatin. Dual-luciferase assay and chromatin co-immunoprecipitation (ChIP) assays confirmed the binding relationship between MEIS2 and ELF1. The results of rescue assay showed that ELF1 could promote DNA damage and enhance the sensitivity of tumor cells to cisplatin by activating MEIS2. In conclusion, the results of this study demonstrated that ELF1 could modulate DNA damage through activating MEIS2 and thus enhance cisplatin sensitivity in prostate cancer. This study suggested that the ELF1/MEIS2 axis may be a therapeutic target to strengthen cisplatin sensitivity in prostate cancer.
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Affiliation(s)
- Dengjun Han
- Urology Department, Zigong Fourth People's Hospital, No.19 Tanmulin Street, Ziliujing District, Zigong City, Sichuan Province 643000, China
| | - Xianyong Li
- Urology Department, Zigong Fourth People's Hospital, No.19 Tanmulin Street, Ziliujing District, Zigong City, Sichuan Province 643000, China
| | - Yang Cheng
- Urology Department, Zigong Fourth People's Hospital, No.19 Tanmulin Street, Ziliujing District, Zigong City, Sichuan Province 643000, China
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Wu MM, Chen CW, Chen CY, Lee CH, Chou M, Hsu LI, Lee TC, Chen CJ. TIMP3 Gene Polymorphisms of -1296 T > C and -915 A > G Increase the Susceptibility to Arsenic-Induced Skin Cancer: A Cohort Study and In Silico Analysis of Mutation Impacts. Int J Mol Sci 2022; 23:ijms232314980. [PMID: 36499314 PMCID: PMC9735753 DOI: 10.3390/ijms232314980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
Long-term exposure to arsenic may induce several human cancers, including non-melanoma skin cancer. The tissue inhibitor of metalloproteinase (TIMP)-3, encoded by the TIMP3 gene, may inhibit tumor growth, invasion, and metastasis of several cancer types. In this study, we aimed to investigate effects of the TIMP3 -1296 T > C (rs9619311) and -915 A > G (rs2234921) single-nucleotide polymorphisms (SNPs) on skin cancer risk in an arsenic-exposed population, and to evaluate the influence of allele-specific changes by an in silico analysis. In total, 1078 study participants were followed up for a median of 15 years for newly diagnosed skin cancer. New cases were identified through linkage to the National Cancer Registry of Taiwan. A Cox regression analysis was used to evaluate the effects of TIMP3 variants. Transcription factor (TF) profiling of binding sites of allele-specific changes in SNPs was conducted using the JASPAR scan tool. We observed borderline associations between TIMP3 genotypes and skin cancer risk. However, when combined with high arsenic exposure levels, the rs9619311 C allele, rs2234921 G allele, or C-G haplotype groups exhibited a greater risk of developing skin cancer compared to the respective common homozygous genotype group. The in silico analysis revealed several TF motifs located at or flanking the two SNP sites. We validated that the C allele of rs9619311 attenuated the binding affinity of BACH2, MEIS2, NFE2L2, and PBX2 to the TIMP3 promoter, and that the G allele of rs2234921 reduced the affinity of E2F8 and RUNX1 to bind to the promoter. Our findings suggest significant modifications of the effect of the association between arsenic exposure and skin cancer risk by the TIMP3 rs9619311 and rs2234921 variants. The predicted TFs and their differential binding affinities to the TIMP3 promoter provide insights into how TIMP3 interacts with arsenic through TFs in skin cancer formation.
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Affiliation(s)
- Meei-Maan Wu
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Master Program in Applied Molecular Epidemiology, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
- School of Public Health, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence:
| | - Chi-Wei Chen
- Department of Life Science, College of Sciences and Engineering, National Dong Hwa University, Hualien 97430, Taiwan
| | - Chiu-Yi Chen
- Master Program in Applied Molecular Epidemiology, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Hung Lee
- Department of Dermatology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 83325, Taiwan
| | - Mark Chou
- School of Public Health, College of Public Health, Taipei Medical University, Taipei 11031, Taiwan
| | - Ling-I Hsu
- Department of Research, Taiwan Blood Services Foundation, Taipei 10066, Taiwan
| | - Te-Chang Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chien-Jen Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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Zhong ME, Huang ZP, Wang X, Cai D, Li CH, Gao F, Wu XJ, Wang W. A Transcription Factor Signature Can Identify the CMS4 Subtype and Stratify the Prognostic Risk of Colorectal Cancer. Front Oncol 2022; 12:902974. [PMID: 35847938 PMCID: PMC9280271 DOI: 10.3389/fonc.2022.902974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundColorectal cancer (CRC) is a heterogeneous disease, and current classification systems are insufficient for stratifying patients with different risks. This study aims to develop a generalized, individualized prognostic consensus molecular subtype (CMS)-transcription factors (TFs)-based signature that can predict the prognosis of CRC.MethodsWe obtained differentially expressed TF signature and target genes between the CMS4 and other CMS subtypes of CRC from The Cancer Genome Atlas (TCGA) database. A multi-dimensional network inference integrative analysis was conducted to identify the master genes and establish a CMS4-TFs-based signature. For validation, an in-house clinical cohort (n = 351) and another independent public CRC cohort (n = 565) were applied. Gene set enrichment analysis (GSEA) and prediction of immune cell infiltration were performed to interpret the biological significance of the model.ResultsA CMS4-TFs-based signature termed TF-9 that includes nine TF master genes was developed. Patients in the TF-9 high-risk group have significantly worse survival, regardless of clinical characteristics. The TF-9 achieved the highest mean C-index (0.65) compared to all other signatures reported (0.51 to 0.57). Immune infiltration revealed that the microenvironment in the high-risk group was highly immune suppressed, as evidenced by the overexpression of TIM3, CD39, and CD40, suggesting that high-risk patients may not directly benefit from the immune checkpoint inhibitors.ConclusionsThe TF-9 signature allows a more precise categorization of patients with relevant clinical and biological implications, which may be a valuable tool for improving the tailoring of therapeutic interventions in CRC patients.
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Affiliation(s)
- Min-Er Zhong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Ping Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xun Wang
- Department of Biomedical Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Du Cai
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng-Hang Li
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Wei Wang, ; Xiao-Jian Wu, ; Feng Gao,
| | - Xiao-Jian Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Wei Wang, ; Xiao-Jian Wu, ; Feng Gao,
| | - Wei Wang
- Biomedical Big Data Centre, Department of Gynaecology, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
- *Correspondence: Wei Wang, ; Xiao-Jian Wu, ; Feng Gao,
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Pastorino L, Grillo F, Albertelli M, Ghiorzo P, Bruno W. Insights into Mechanisms of Tumorigenesis in Neuroendocrine Neoplasms. Int J Mol Sci 2021; 22:ijms221910328. [PMID: 34638668 PMCID: PMC8508699 DOI: 10.3390/ijms221910328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Genomic studies have identified some of the most relevant genetic players in Neuroendocrine Neoplasm (NEN) tumorigenesis. However, we are still far from being able to draw a model that encompasses their heterogeneity, elucidates the different biological effects consequent to the identified molecular events, or incorporates extensive knowledge of molecular biomarkers and therapeutic targets. Here, we reviewed recent insights in NEN tumorigenesis from selected basic research studies on animal models, highlighting novel players in the intergenic cooperation and peculiar mechanisms including splicing dysregulation, chromatin stability, or cell dedifferentiation. Furthermore, models of tumorigenesis based on composite interactions other than a linear progression of events are proposed, exemplified by the involvement in NEN tumorigenesis of genes regulating complex functions, such as MEN1 or DAXX. Although limited by interspecies differences, animal models have proved helpful for the more in-depth study of every facet of tumorigenesis, showing that the identification of driver mutations is only one of the many necessary steps and that other mechanisms are worth investigating.
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Affiliation(s)
- Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
| | - Federica Grillo
- Anatomic Pathology Unit, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy;
- Anatomic Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 1632 Genoa, Italy
| | - Manuela Albertelli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
- Endocrinology Unit, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genoa, Italy; (L.P.); (P.G.)
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy;
- Correspondence: ; Tel.: +39-(01)-0555-7254
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8
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Pan Z, He Y, Zhu W, Xu T, Hu X, Huang P. A Dynamic Transcription Factor Signature Along the Colorectal Adenoma-Carcinoma Sequence in Patients With Co-Occurrent Adenoma and Carcinoma. Front Oncol 2021; 11:597447. [PMID: 34094897 PMCID: PMC8176860 DOI: 10.3389/fonc.2021.597447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 03/31/2021] [Indexed: 12/24/2022] Open
Abstract
Background Colorectal carcinoma (CRC) often arises from benign adenoma after a stepwise accumulation of genetic alterations. Here, we profiled the dynamic landscapes of transcription factors (TFs) in the mucosa-adenoma-carcinoma progression sequence. Methods The transcriptome data of co-occurrent adenoma, carcinoma, and normal mucosa samples were obtained from GSE117606. Identification of differentially expressed TFs (DE-TFs) and subsequent function annotation were conducted in R software. Expression patterns of DE-TFs were clustered by Short Time-series Expression Miner software. Thereafter, modular co-expression analysis, Kaplan-Meier survival analysis, mutation profiling, and gene set enrichment analysis were conducted to investigate TF dynamics in colorectal tumorigenesis. Finally, tissue microarrays, including 51 tumors, 32 adenomas, and 53 normal tissues, were employed to examine the expression of significant candidates by immunohistochemistry staining. Results Compared to normal tissues, 20 (in adenoma samples) and 29 (in tumor samples) DE-TFs were identified. During the disease course, 28 expression patterns for DE-TFs and four co-expression modules were clustered. Notably, six DE-TFs, DACH1, GTF2IRD1, MEIS2, NR3C2, SOX9, and SPIB, were identified as having a dynamic signature along the colorectal adenoma-carcinoma sequence. The dynamic signature was of significance in GO enrichment, prognosis, and co-expression analysis. Among the 6-TF signature, the roles of GTF2IRD1, SPIB and NR3C2 in CRC progression are unclear. Immunohistochemistry validation showed that GTF2IRD1 enhanced significantly throughout the mucosa-adenoma-carcinoma sequence, while SPIB and NR3C2 kept decreasing in stroma during the disease course. Conclusions Our study provided a dynamic 6-TF signature throughout the course of colorectal mucosa-adenoma-carcinoma. These findings deepened the understanding of colorectal cancer pathogenesis.
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Affiliation(s)
- Zongfu Pan
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Ying He
- Central Laboratory, First Affiliated Hospital, Huzhou University, The First People's Hospital of Huzhou, Huzhou, China
| | - Wenjuan Zhu
- Department of Pathology, First Affiliated Hospital, Huzhou University, The First People's Hospital of Huzhou, Huzhou, China
| | - Tong Xu
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Xiaoping Hu
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Ping Huang
- Department of Pharmacy, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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9
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Poturnajova M, Furielova T, Balintova S, Schmidtova S, Kucerova L, Matuskova M. Molecular features and gene expression signature of metastatic colorectal cancer (Review). Oncol Rep 2021; 45:10. [PMID: 33649827 PMCID: PMC7876998 DOI: 10.3892/or.2021.7961] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 12/04/2020] [Indexed: 12/13/2022] Open
Abstract
Uncontrollable metastatic outgrowth process is the leading cause of mortality worldwide, even in the case of colorectal cancer. Colorectal cancer (CRC) accounts for approximately 10% of all annually diagnosed cancers and 50% of CRC patients will develop metastases in the course of disease. Most patients with metastatic CRC have incurable disease. Even if patients undergo resection of liver metastases, the 5‑year survival rate ranges from 25 to 58%. Next‑generation sequencing of tumour specimens from large colorectal cancer patient cohorts has led to major advances in elucidating the genomic landscape of these tumours and paired metastases. The expression profiles of primary CRC and their metastatic lesions at both the gene and pathway levels were compared and led to the selection of early driver genes responsible for carcinogenesis and metastasis‑specific genes that increased the metastatic process. The genetic, transcriptional and epigenetic alteration encoded by these genes and their combination influence many pivotal signalling pathways, enabling the dissemination and outgrowth in distant organs. Therapeutic regimens affecting several different active pathways may have important implications for therapeutic efficacy.
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Affiliation(s)
- Martina Poturnajova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, University Science Park for Biomedicine, 84505 Bratislava, Slovakia
| | - Tatiana Furielova
- Department of Genetics, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Sona Balintova
- Department of Genetics, Faculty of Natural Sciences, Comenius University, 84215 Bratislava, Slovakia
| | - Silvia Schmidtova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, University Science Park for Biomedicine, 84505 Bratislava, Slovakia
- Translational Research Unit, Faculty of Medicine, Comenius University, 81499 Bratislava, Slovakia
| | - Lucia Kucerova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, University Science Park for Biomedicine, 84505 Bratislava, Slovakia
| | - Miroslava Matuskova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, University Science Park for Biomedicine, 84505 Bratislava, Slovakia
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10
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Gİrgİn B, KaradaĞ-Alpaslan M, KocabaŞ F. Oncogenic and tumor suppressor function of MEIS and associated factors. ACTA ACUST UNITED AC 2021; 44:328-355. [PMID: 33402862 PMCID: PMC7759197 DOI: 10.3906/biy-2006-25] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
MEIS proteins are historically associated with tumorigenesis, metastasis, and invasion in cancer. MEIS and associated PBX-HOX proteins may act as tumor suppressors or oncogenes in different cellular settings. Their expressions tend to be misregulated in various cancers. Bioinformatic analyses have suggested their upregulation in leukemia/lymphoma, thymoma, pancreas, glioma, and glioblastoma, and downregulation in cervical, uterine, rectum, and colon cancers. However, every cancer type includes, at least, a subtype with high MEIS expression. In addition, studies have highlighted that MEIS proteins and associated factors may function as diagnostic or therapeutic biomarkers for various diseases. Herein, MEIS proteins and associated factors in tumorigenesis are discussed with recent discoveries in addition to how they could be modulated by noncoding RNAs or newly developed small-molecule MEIS inhibitors.
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Affiliation(s)
- Birkan Gİrgİn
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
| | - Medine KaradaĞ-Alpaslan
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayıs University, Samsun Turkey
| | - Fatih KocabaŞ
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbul Turkey.,Graduate School of Natural and Applied Sciences, Yeditepe University, İstanbul Turkey.,Meinox Pharma Technologies, İstanbul Turkey
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11
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Fiannaca A, Paglia LL, Rosa ML, Rizzo R, Urso A. miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions. BMC Bioinformatics 2020; 21:199. [PMID: 32938402 PMCID: PMC7493844 DOI: 10.1186/s12859-020-3520-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interaction with a miRNAs-response element. Other RNA molecules participate in the complex network of gene regulation. They behave as competitive endogenous RNA (ceRNA), acting as natural miRNA sponges to inhibit miRNA functions and modulate the expression of RNA messenger (mRNA). It became evident that understanding the ceRNA-miRNA-mRNA crosstalk would increase the functional information across the transcriptome, contributing to identify new potential biomarkers for translational medicine. RESULTS We present miRTissue ce, an improvement of our original miRTissue web service. By introducing a novel computational pipeline, miRTissue ce provides an easy way to search for ceRNA interactions in several cancer tissue types. Moreover it extends the functionalities of previous miRTissue release about miRNA-target interaction in order to provide a complete insight about miRNA mediated regulation processes. miRTissue ce is freely available at http://tblab.pa.icar.cnr.it/mirtissue.html . CONCLUSIONS The study of ceRNA networks and its dynamics in cancer tissue could be applied in many fields of translational biology, as the investigation of new cancer biomarker, both diagnostic and prognostic, and also in the investigation of new therapeutic strategies of intervention. In this scenario, miRTissue ce can offer a powerful instrument for the analysis and characterization of ceRNA-ceRNA interactions in different tissue types, representing a fundamental step in order to understand more complex regulation mechanisms.
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Affiliation(s)
- Antonino Fiannaca
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Laura La Paglia
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Massimo La Rosa
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Riccardo Rizzo
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Alfonso Urso
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
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12
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Wang X, Hao R, Wang F, Wang F. ZFAS1 Promotes Cisplatin Resistance via Suppressing miR-421 Expression in Oral Squamous Cell Carcinoma. Cancer Manag Res 2020; 12:7251-7262. [PMID: 32884341 PMCID: PMC7434533 DOI: 10.2147/cmar.s248869] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/03/2020] [Indexed: 12/28/2022] Open
Abstract
Purpose Oral squamous cell carcinoma (OSCC), with high incidence and mortality, represents one of the main reasons for head and neck malignant tumors. We want to investigate the effect of ZFAS1 on DDP resistance in oral squamous cell carcinoma. Methods The proliferation and migration of cells was detected by CCK-8 and Transwell assay. The apoptosis was measured by flow cytometry and Western blot. The interaction of ZFAS1, miR-421, and MEIS2 was verified by luciferase reporter assay. The role of ZFAS1 in DDP resistance in vivo was tested by the nude mice model. The expression of ZFAS1 in exosomes from cisplatin-resistant patients was also determined. Results ZFAS1 overexpression improved OSCC cell growth and inhibited OSCC cell susceptibility to DDP. In addition, the silencing of ZFAS1 promoted DDP-induced apoptosis. ZFAS1 directly bound to miR-421, which was verified by luciferase reporter assay. Inhibition of miR-421 reversed the effect of si-ZFAS1, which promoted the cell viability and decreased the sensitivity of DDP in DDP-resistant cells. The in vivo experiment showed the role of ZFAS1 in increasing the DDP resistance in OSCC tumor. Importantly, this study also showed upregulated ZFAS1 in serum exosomes derived from cisplatin-resistant patients. Conclusion ZFAS1 promotes chemoresistance of oral squamous cell carcinoma to cisplatin and might become a latent therapeutic target for treating OSCC.
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Affiliation(s)
- Xiaolong Wang
- Department of Stomatology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, People's Repubic of China
| | - Rui Hao
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, People's Repubic of China
| | - Fengjuan Wang
- Department of Stomatology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, People's Repubic of China
| | - Fan Wang
- Department of Stomatology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, People's Repubic of China
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Xu L, Bi Y, Xu Y, Zhang Z, Xu W, Zhang S, Chen J. Oridonin inhibits the migration and epithelial-to-mesenchymal transition of small cell lung cancer cells by suppressing FAK-ERK1/2 signalling pathway. J Cell Mol Med 2020; 24:4480-4493. [PMID: 32168416 PMCID: PMC7176879 DOI: 10.1111/jcmm.15106] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/12/2020] [Accepted: 01/31/2020] [Indexed: 12/16/2022] Open
Abstract
Small cell lung cancer (SCLC) is a severe malignant with high morbidity; however, few effective and secure therapeutic strategy is used in current clinical practice. Oridonin is a small molecule from the traditional Chinese herb Rabdosia rubescens. This study mainly aimed to investigate the role of oridonin on inhibiting the process of H1688, a kind of small cell lung cancer cells from human. Oridonin could suppress H1688 cell proliferation and induce their apoptosis in a high dosage treatment (20 μmol/L). Meanwhile, cell migration was suppressed by oridonin (5 and 10 μmol/L) that did not affect cell proliferation and apoptosis. The expression level of E-cadherin was significantly increased, and the expression of vimentin, snail and slug was reduced after administration of oridonin. These expression changes were associated with the suppressed integrin β1, phosphorylation of focal adhesion kinase (FAK) and ERK1/2. In addition, oridonin (5 and 10 mg/kg) inhibited tumour growth in a nude mouse model; however, HE staining revealed a certain degree of cytotoxicity in hepatic tissue after treatment oridonin (10 mg/kg). Furthermore, the concentration of alanine aminotransferase (ALP) was significantly increased and lactate dehydrogenase (LDH) was reduced after oridonin treatment (10 mg/kg). Immunohistochemical analysis further revealed that oridonin increased E-cadherin expression and reduced vimentin and phospho-FAK levels in vivo. These findings indicated that oridonin can inhibit the migration and epithelial-to-mesenchymal transition (EMT) of SCLC cells by suppressing the FAK-ERK1/2 signalling pathway. Thus, oridonin may be a new drug candidate to offer an effect of anti-SCLC with relative safety.
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Affiliation(s)
- Linhao Xu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, China.,Translational Medicine Research Center, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanli Bi
- Department of Clinical Laboratorial Examination, Air Force Hangzhou Special Service Recuperation Center Sanatorium Area 3, Hangzhou, China
| | - Yizhou Xu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhuocheng Zhang
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Wenjie Xu
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Sisi Zhang
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Jian Chen
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, China
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14
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Nørgaard M, Haldrup C, Bjerre MT, Høyer S, Ulhøi B, Borre M, Sørensen KD. Epigenetic silencing of MEIS2 in prostate cancer recurrence. Clin Epigenetics 2019; 11:147. [PMID: 31640805 PMCID: PMC6805635 DOI: 10.1186/s13148-019-0742-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023] Open
Abstract
Background Current diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, resulting in overdiagnosis and overtreatment of clinically insignificant tumors. Thus, to improve the management of PC, novel biomarkers are urgently needed. Results In this study, we integrated genome-wide methylome (Illumina 450K DNA methylation array (450K)) and RNA sequencing (RNAseq) data performed in a discovery set of 27 PC and 15 adjacent normal (AN) prostate tissue samples to identify candidate driver genes involved in PC development and/or progression. We found significant enrichment for homeobox genes among the most aberrantly methylated and transcriptionally dysregulated genes in PC. Specifically, homeobox gene MEIS2 (Myeloid Ecotropic viral Insertion Site 2) was significantly hypermethylated (p < 0.0001, Mann-Whitney test) and transcriptionally downregulated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue in our discovery sample set, which was also confirmed in an independent validation set including > 500 PC and AN tissue samples in total (TCGA cohort analyzed by 450K and RNAseq). Furthermore, in three independent radical prostatectomy (RP) cohorts (n > 700 patients in total), low MEIS2 transcriptional expression was significantly associated with poor biochemical recurrence (BCR) free survival (p = 0.0084, 0.0001, and 0.0191, respectively; log-rank test). Next, we analyzed another RP cohort consisting of > 200 PC, AN, and benign prostatic hyperplasia (BPH) samples by quantitative methylation-specific PCR (qMSP) and found that MEIS2 was significantly hypermethylated (p < 0.0001, Mann-Whitney test) in PC compared to non-malignant prostate tissue samples (AN and BPH) with an AUC > 0.84. Moreover, in this cohort, aberrant MEIS2 hypermethylation was significantly associated with post-operative BCR (p = 0.0068, log-rank test), which was subsequently confirmed (p = 0.0067; log-rank test) in the independent TCGA validation cohort (497 RP patients; 450K data). Conclusions To the best of our knowledge, this is the first study to investigate, demonstrate, and independently validate a prognostic biomarker potential for MEIS2 at the transcriptional expression level and at the DNA methylation level in PC.
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Affiliation(s)
- Maibritt Nørgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Christa Haldrup
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marianne Trier Bjerre
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Høyer
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Benedicte Ulhøi
- Department of Histopathology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark. .,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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