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Kaushal JB, Takkar S, Batra SK, Siddiqui JA. Diverse landscape of genetically engineered mouse models: Genomic and molecular insights into prostate cancer. Cancer Lett 2024; 593:216954. [PMID: 38735382 DOI: 10.1016/j.canlet.2024.216954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/14/2024]
Abstract
Prostate cancer (PCa) is a significant health concern for men worldwide and is particularly prevalent in the United States. It is a complex disease presenting different molecular subtypes and varying degrees of aggressiveness. Transgenic/genetically engineered mouse models (GEMMs) greatly enhanced our understanding of the intricate molecular processes that underlie PCa progression and have offered valuable insights into potential therapeutic targets for this disease. The integration of whole-exome and whole-genome sequencing, along with expression profiling, has played a pivotal role in advancing GEMMs by facilitating the identification of genetic alterations driving PCa development. This review focuses on genetically modified mice classified into the first and second generations of PCa models. We summarize whether models created by manipulating the function of specific genes replicate the consequences of genomic alterations observed in human PCa, including early and later disease stages. We discuss cases where GEMMs did not fully exhibit the expected human PCa phenotypes and possible causes of the failure. Here, we summarize the comprehensive understanding, recent advances, strengths and limitations of the GEMMs in advancing our insights into PCa, offering genetic and molecular perspectives for developing novel GEMM models.
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Affiliation(s)
- Jyoti B Kaushal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Simran Takkar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA.
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA.
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Myers MA, Arnold BJ, Bansal V, Balaban M, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. Genome Biol 2024; 25:130. [PMID: 38773520 PMCID: PMC11110434 DOI: 10.1186/s13059-024-03267-x] [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: 07/13/2023] [Accepted: 05/03/2024] [Indexed: 05/24/2024] Open
Abstract
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HATCHet2, an algorithm to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 extends the earlier HATCHet method by improving identification of focal CNAs and introducing a novel statistic, the minor haplotype B-allele frequency (mhBAF), that enables identification of mirrored-subclonal CNAs. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 10 prostate cancer patients reveals previously unreported mirrored-subclonal CNAs affecting cancer genes.
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Affiliation(s)
- Matthew A Myers
- Department of Computer Science, Princeton University, Princeton, USA
| | - Brian J Arnold
- Center for Statistics and Machine Learning, Princeton University, Princeton, USA
| | - Vineet Bansal
- Princeton Research Computing, Princeton University, Princeton, NJ, USA
| | - Metin Balaban
- Department of Computer Science, Princeton University, Princeton, USA
| | - Katelyn M Mullen
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Zaccaria
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
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Schitcu VH, Raduly L, Zanoaga O, Jurj A, Munteanu VC, Budisan L, Petrut B, Braicu C, Coman I, Berindan-Neagoe I. TP53 gene implications in prostate cancer evolution: potential role in tumor classification. Med Pharm Rep 2023; 96:384-391. [PMID: 37970196 PMCID: PMC10642740 DOI: 10.15386/mpr-2639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/01/2023] [Accepted: 07/13/2023] [Indexed: 11/17/2023] Open
Abstract
Background and aims Prostate adenocarcinoma (PRAD) is a complex disease that can be driven by alterations in both coding and noncoding genes. Recent research has identified coding and non-coding genes that are considered to play important roles in prostate cancer evolution and which may be used as biomarkers for disease diagnosis, prognosis, and treatment. TP53 is a critical hub gene in prostate cancer. Advanced studies have demonstrated the crosstalk between coding and non-coding RNAs, particularly microRNAs (miRNAs). Methods In this study, we investigated the roundabout of TP53 and their regulatory miRNAs (miR-15a-5p, miR-34a-5p, and miR-141-3p) based on the TCGA data set. We validated an additional patient cohort of 28 matched samples of patients with PRAD at tissue and plasma level. Results Therefore, using the UALCAN online database, we evaluated the expression level in PRAD of these genes revealing overexpression of TP53. qRT-PCR validation step endorsed the expression level for these genes. Additionally, we evaluated the expression level of the four key miRNAs (miR-15a-5p, miR-34a-5p, and miR-141-3p) interconnected as a network at tissue and plasma levels. Conclusions Through these results, we demonstrated the essential function of TP53 and its associated miRNAs that play a significant role in tumor control, highlighting miRNAs' potential as future therapeutic targets and biomarkers with important implications in managing prostate cancer.
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Affiliation(s)
- Vlad Horia Schitcu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Urology, “Prof. Dr. Ion Chiricuta” Oncology Institute, Cluj-Napoca, Romania
- Department of Urology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Oana Zanoaga
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Vlad Cristian Munteanu
- Department of Urology, “Prof. Dr. Ion Chiricuta” Oncology Institute, Cluj-Napoca, Romania
- Department of Urology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Liviuta Budisan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bogdan Petrut
- Department of Urology, “Prof. Dr. Ion Chiricuta” Oncology Institute, Cluj-Napoca, Romania
- Department of Urology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioan Coman
- Department of Urology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Zoroddu S, Sanna L, Bordoni V, Lyu W, Murineddu G, Pinna GA, Forcales SV, Sala A, Kelvin DJ, Bagella L. RNAseq Analysis of Novel 1,3,4-Oxadiazole Chalcogen Analogues Reveals Anti-Tubulin Properties on Cancer Cell Lines. Int J Mol Sci 2023; 24:11263. [PMID: 37511023 PMCID: PMC10379353 DOI: 10.3390/ijms241411263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
1,3,4-Oxadiazole derivatives are among the most studied anticancer drugs. Previous studies have analyzed the action of different 1,3,4-oxadiazole derivatives and their effects on cancer cells. This study investigated the characterization of two new compounds named 6 and 14 on HeLa and PC-3 cancer cell lines. Based on the previously obtained IC50, cell cycle effects were monitored by flow cytometry. RNA sequencing (RNAseq) was performed to identify differentially expressed genes, followed by functional annotation using gene ontology (GO), KEGG signaling pathway enrichment, and protein-protein interaction (PPI) network analyses. The tubulin polymerization assay was used to analyze the interaction of both compounds with tubulin. The results showed that 6 and 14 strongly inhibited the proliferation of cancer cells by arresting them in the G2/M phase of the cell cycle. Transcriptome analysis showed that exposure of HeLa and PC-3 cells to the compounds caused a marked reprograming of gene expression. Functional enrichment analysis indicated that differentially expressed genes were significantly enriched throughout the cell cycle and cancer-related biological processes. Furthermore, PPI network, hub gene, and CMap analyses revealed that compounds 14 and 6 shared target genes with established microtubule inhibitors, indicating points of similarity between the two molecules and microtubule inhibitors in terms of the mechanism of action. They were also able to influence the polymerization process of tubulin, suggesting the potential of these new compounds to be used as efficient chemotherapeutic agents.
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Affiliation(s)
- Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Luca Sanna
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Valentina Bordoni
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
| | - Weidong Lyu
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, China
| | - Gabriele Murineddu
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Gerard A Pinna
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Sonia Vanina Forcales
- Department of Pathology and Experimental Therapeutics, School of Medicine, Health Science Campus of Bellvitge, University of Barcelona, Carrer de la Feixa Llarga, s/n, Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Arturo Sala
- Centre for Inflammation Research and Translational Medicine (CIRTM), Department of Life Sciences, Brunel University, London UB8 3PH, UK
| | - David J Kelvin
- Division of Immunology, International Institute of Infection and Immunity, Shantou University Medical College, Shantou 515031, China
- Department of Microbiology and Immunology, Dalhousie University, 6299 South St, Halifax, NS B3H 4R2, Canada
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Centre for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Xu H, Luo W, Zhao Z, Miao X, Chai C, Hu J, Tang H, Zhang H, Zhou W. Establishment and characterization of a new intrahepatic cholangiocarcinoma cell line, ICC-X3. Hum Cell 2023; 36:854-865. [PMID: 36662372 DOI: 10.1007/s13577-023-00858-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/14/2023] [Indexed: 01/21/2023]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is an aggressive cancer of the biliary tract that is prone to recurrence and metastasis and is characterized by poor sensitivity to chemotherapy and overall prognosis. To address this challenge, the establishment of suitable preclinical models is critical. In this study, we successfully established a new ICC cell line, named ICC-X3, from the satellite lesions of one ICC patient. The cell line was characterized with respect to phenotypic, molecular, biomarker, functional and histological properties. STR confirmed that ICC-X3 was highly consistent with primary tumor tissue. ICC-X3 cells positively expressed CK7, CK19, E-cadherin, vimentin, and Ki67. ICC-X3 was all resistant to gemcitabine, paclitaxel, 5-FU, and oxaliplatin. The cell line was able to rapidly form xenograft tumors which were highly similar to the primary tumor. The missense mutation of TP53 exon was detected in ICC-X3 cells. ICC-X3 can be used as a good experimental model to study the progression, metastasis, and drug resistance of ICC.
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Affiliation(s)
- Hao Xu
- The Forth Department of General Surgery, the First Hospital of Lanzhou University, No. 1, Donggang West Road, LanZhou, 730000, Gansu, China.
| | - Wei Luo
- The Forth Department of General Surgery, the First Hospital of Lanzhou University, No. 1, Donggang West Road, LanZhou, 730000, Gansu, China
| | - Zhenjie Zhao
- The Forth Department of General Surgery, the First Hospital of Lanzhou University, No. 1, Donggang West Road, LanZhou, 730000, Gansu, China
| | - Xin Miao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, LanZhou, 730000, China
| | - Changpeng Chai
- The Forth Department of General Surgery, the First Hospital of Lanzhou University, No. 1, Donggang West Road, LanZhou, 730000, Gansu, China
| | - Jinjing Hu
- The Forth Department of General Surgery, the First Hospital of Lanzhou University, No. 1, Donggang West Road, LanZhou, 730000, Gansu, China
| | - Huan Tang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
| | - Hui Zhang
- Department of General Surgery, the Second Hospital of Lanzhou University, Lanzhou, 730000, China.
| | - Wence Zhou
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, China.
- Department of General Surgery, the Second Hospital of Lanzhou University, Lanzhou, 730000, China.
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Xu X, Xie L, Meng L, Geng S, Liu J, Cao X, Dong Z, Xing Z. Genetic features of TP53 mutation and its downstream FOXA1 in prostate cancer. Biosci Trends 2022; 16:221-229. [PMID: 35768267 DOI: 10.5582/bst.2022.01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xiaofei Xu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong, China
| | - Limei Xie
- Department of Public Health, The Second Hospital of Shandong University, Ji'nan, Shandong, China
| | - Liwei Meng
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, Shandong, China
| | - Shangzhen Geng
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, Shandong, China
| | - Jin Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong, China
| | - Xiangting Cao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong, China
| | - Zhaogang Dong
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Ji'nan, Shandong, China
| | - Zhaoquan Xing
- Department of Urology, Qilu Hospital of Shandong University, Ji'nan, Shandong, China
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