1
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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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2
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Sánchez-Marín D, Silva-Cázares MB, Porras-Reyes FI, García-Román R, Campos-Parra AD. Breaking paradigms: Long non-coding RNAs forming gene fusions with potential implications in cancer. Genes Dis 2024; 11:101136. [PMID: 38292185 PMCID: PMC10825296 DOI: 10.1016/j.gendis.2023.101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/16/2023] [Accepted: 09/10/2023] [Indexed: 02/01/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs longer than 200 nucleotides with dynamic regulatory functions. They interact with a wide range of molecules such as DNA, RNA, and proteins to modulate diverse cellular functions through several mechanisms and, if deregulated, they can lead to cancer development and progression. Recently, it has been described that lncRNAs are susceptible to form gene fusions with mRNAs or other lncRNAs, breaking the paradigm of gene fusions consisting mainly of protein-coding genes. However, their biological significance in the tumor phenotype is still uncertain. Therefore, their recent identification opens a new line of research to study their biological role in tumorigenesis, and their potential as biomarkers with clinical relevance or as therapeutic targets. The present study aimed to review the lncRNA fusions identified so far and to know which of them have been associated with a potential function. We address the current challenges to deepen their study as well as the reasons why they represent a future therapeutic window in cancer.
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Affiliation(s)
- David Sánchez-Marín
- Posgrado en Ciencias Biológicas, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04360, México
| | - Macrina Beatriz Silva-Cázares
- Unidad Académica Multidisciplinaria Región Altiplano, Universidad Autónoma de San Luis Potosí (UASLP), Carretera a Cedral Km 5+600, Ejido San José de la Trojes, Matehuala, San Luis Potosí, C.P. 78760, México
| | - Fany Iris Porras-Reyes
- Servicio de Anatomía Patológica, Instituto Nacional de Cancerología (INCan), Niño Jesús, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Rebeca García-Román
- Instituto de Salud Pública, Universidad Veracruzana (UV), Av. Dr Luis, Dr. Castelazo Ayala s/n, Col. Industrial Ánimas, Xalapa, Veracruz, C.P. 91190, México
| | - Alma D. Campos-Parra
- Instituto de Salud Pública, Universidad Veracruzana (UV), Av. Dr Luis, Dr. Castelazo Ayala s/n, Col. Industrial Ánimas, Xalapa, Veracruz, C.P. 91190, México
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3
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Kasi PM, Lee JK, Pasquina LW, Decker B, Vanden Borre P, Pavlick DC, Allen JM, Parachoniak C, Quintanilha JCF, Graf RP, Schrock AB, Oxnard GR, Lovly CM, Tukachinsky H, Subbiah V. Circulating Tumor DNA Enables Sensitive Detection of Actionable Gene Fusions and Rearrangements Across Cancer Types. Clin Cancer Res 2024; 30:836-848. [PMID: 38060240 PMCID: PMC10870120 DOI: 10.1158/1078-0432.ccr-23-2693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/03/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
PURPOSE Genomic rearrangements can generate potent oncogenic drivers or disrupt tumor suppressor genes. This study examines the landscape of fusions and rearrangements detected by liquid biopsy (LBx) of circulating tumor DNA (ctDNA) across different cancer types. EXPERIMENTAL DESIGN LBx from 53,842 patients with 66 solid tumor types were profiled using FoundationOneLiquid CDx, a hybrid-capture sequencing platform that queries 324 cancer-related genes. Tissue biopsies (TBx) profiled using FoundationOneCDx were used as a comparator. RESULTS Among all LBx, 7,377 (14%) had ≥1 pathogenic rearrangement detected. A total of 3,648 (6.8%) LBx had ≥1 gain-of-function (GOF) oncogene rearrangement, and 4,428 (8.2%) LBx had ≥1 loss-of-function rearrangement detected. Cancer types with higher prevalence of GOF rearrangements included those with canonical fusion drivers: prostate cancer (19%), cholangiocarcinoma (6.4%), bladder (5.5%), and non-small cell lung cancer (4.4%). Although the prevalence of driver rearrangements was lower in LBx than TBx overall, the frequency of detection was comparable in LBx with a tumor fraction (TF) ≥1%. Rearrangements in FGFR2, BRAF, RET, and ALK, were detected across cancer types, but tended to be clonal variants in some cancer types and potential acquired resistance variants in others. CONCLUSIONS In contrast to some prior literature, this study reports detection of a wide variety of rearrangements in ctDNA. The prevalence of driver rearrangements in tissue and LBx was comparable when TF ≥1%. LBx presents a viable alternative when TBx is not available, and there may be less value in confirmatory testing when TF is sufficient.
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Affiliation(s)
- Pashtoon M. Kasi
- Weill Cornell Medicine, Englander Institute of Precision Medicine, New York Presbyterian Hospital, New York, New York
| | | | | | | | | | | | | | | | | | - Ryon P. Graf
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, Texas
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4
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Chehelgerdi M, Behdarvand Dehkordi F, Chehelgerdi M, Kabiri H, Salehian-Dehkordi H, Abdolvand M, Salmanizadeh S, Rashidi M, Niazmand A, Ahmadi S, Feizbakhshan S, Kabiri S, Vatandoost N, Ranjbarnejad T. Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy. Mol Cancer 2023; 22:189. [PMID: 38017433 PMCID: PMC10683363 DOI: 10.1186/s12943-023-01873-0] [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: 07/04/2023] [Accepted: 09/27/2023] [Indexed: 11/30/2023] Open
Abstract
The advent of iPSCs has brought about a significant transformation in stem cell research, opening up promising avenues for advancing cancer treatment. The formation of cancer is a multifaceted process influenced by genetic, epigenetic, and environmental factors. iPSCs offer a distinctive platform for investigating the origin of cancer, paving the way for novel approaches to cancer treatment, drug testing, and tailored medical interventions. This review article will provide an overview of the science behind iPSCs, the current limitations and challenges in iPSC-based cancer therapy, the ethical and social implications, and the comparative analysis with other stem cell types for cancer treatment. The article will also discuss the applications of iPSCs in tumorigenesis, the future of iPSCs in tumorigenesis research, and highlight successful case studies utilizing iPSCs in tumorigenesis research. The conclusion will summarize the advancements made in iPSC-based tumorigenesis research and the importance of continued investment in iPSC research to unlock the full potential of these cells.
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Affiliation(s)
- Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Fereshteh Behdarvand Dehkordi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Hamidreza Kabiri
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | | | - Mohammad Abdolvand
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Sharareh Salmanizadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar-Jereeb Street, Isfahan, 81746-73441, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Anoosha Niazmand
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Saba Ahmadi
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Sara Feizbakhshan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Saber Kabiri
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Nasimeh Vatandoost
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tayebeh Ranjbarnejad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
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5
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Myers MA, Arnold BJ, Bansal V, Mullen KM, Zaccaria S, Raphael BJ. HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548855. [PMID: 37502835 PMCID: PMC10370020 DOI: 10.1101/2023.07.13.548855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different numbers of copies of parental haplotypes in different tumor clones. HATCHet2 also has high accuracy in identifying focal CNAs and extends the earlier HATCHet method in several directions. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 50 prostate cancer samples from 10 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
| | - 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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6
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Gioukaki C, Georgiou A, Gkaralea LE, Kroupis C, Lazaris AC, Alamanis C, Thomopoulou GE. Unravelling the Role of P300 and TMPRSS2 in Prostate Cancer: A Literature Review. Int J Mol Sci 2023; 24:11299. [PMID: 37511059 PMCID: PMC10379122 DOI: 10.3390/ijms241411299] [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: 05/31/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Prostate cancer is one of the most common malignant diseases in men, and it contributes significantly to the increased mortality rate in men worldwide. This study aimed to review the roles of p300 and TMPRSS2 (transmembrane protease, serine 2) in the AR (androgen receptor) pathway as they are closely related to the development and progression of prostate cancer. This paper represents a library-based study conducted by selecting the most suitable, up-to-date scientific published articles from online journals. We focused on articles that use similar techniques, particularly those that use prostate cancer cell lines and immunohistochemical staining to study the molecular impact of p300 and TMPRSS2 in prostate cancer specimens. The TMPRSS2:ERG fusion is considered relevant to prostate cancer, but its association with the development and progression as well as its clinical significance have not been fully elucidated. On the other hand, high p300 levels in prostate cancer biopsies predict larger tumor volumes, extraprostatic extension of disease, and seminal vesicle involvement at prostatectomy, and may be associated with prostate cancer progression after surgery. The inhibition of p300 has been shown to reduce the proliferation of prostate cancer cells with TMPRSS2:ETS (E26 transformation-specific) fusions, and combining p300 inhibitors with other targeted therapies may increase their efficacy. Overall, the interplay between the p300 and TMPRSS2 pathways is an active area of research.
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Affiliation(s)
- Charitomeni Gioukaki
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Alexandros Georgiou
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - Christos Kroupis
- Department of Clinical Biochemistry, Attikon University Hospital, National and Kapodistrian University of Athens, 12461 Athens, Greece
| | - Andreas C Lazaris
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christos Alamanis
- 1st Urology Department, Laiko Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Georgia Eleni Thomopoulou
- Cytopathology Department, Attikon University Hospital, National and Kapodistrian University of Athens, 12461 Athens, Greece
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7
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Liu CC, Wang XS. Are cis-spliced fusion proteins pathological in more aggressive luminal breast cancer? Oncotarget 2023; 14:595-596. [PMID: 37306551 PMCID: PMC10259257 DOI: 10.18632/oncotarget.28438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 06/13/2023] Open
Affiliation(s)
| | - Xiao-Song Wang
- Correspondence to:Xiao-Song Wang, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, USA email
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8
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Koistinen H, Kovanen RM, Hollenberg MD, Dufour A, Radisky ES, Stenman UH, Batra J, Clements J, Hooper JD, Diamandis E, Schilling O, Rannikko A, Mirtti T. The roles of proteases in prostate cancer. IUBMB Life 2023; 75:493-513. [PMID: 36598826 PMCID: PMC10159896 DOI: 10.1002/iub.2700] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/22/2022] [Indexed: 01/05/2023]
Abstract
Since the proposition of the pro-invasive activity of proteolytic enzymes over 70 years ago, several roles for proteases in cancer progression have been established. About half of the 473 active human proteases are expressed in the prostate and many of the most well-characterized members of this enzyme family are regulated by androgens, hormones essential for development of prostate cancer. Most notably, several kallikrein-related peptidases, including KLK3 (prostate-specific antigen, PSA), the most well-known prostate cancer marker, and type II transmembrane serine proteases, such as TMPRSS2 and matriptase, have been extensively studied and found to promote prostate cancer progression. Recent findings also suggest a critical role for proteases in the development of advanced and aggressive castration-resistant prostate cancer (CRPC). Perhaps the most intriguing evidence for this role comes from studies showing that the protease-activated transmembrane proteins, Notch and CDCP1, are associated with the development of CRPC. Here, we review the roles of proteases in prostate cancer, with a special focus on their regulation by androgens.
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Affiliation(s)
- Hannu Koistinen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Finland
| | - Ruusu-Maaria Kovanen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland
| | - Morley D Hollenberg
- Department of Physiology & Pharmacology and Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology and Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, U.S.A
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Finland
| | - Jyotsna Batra
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - Judith Clements
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, Australia
| | - John D. Hooper
- Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Eleftherios Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland
- Department of Urology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Mirtti
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland
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9
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Drazdauskienė U, Kapustina Ž, Medžiūnė J, Dubovskaja V, Sabaliauskaitė R, Jarmalaitė S, Lubys A. Fusion sequencing via terminator-assisted synthesis (FTAS-seq) identifies TMPRSS2 fusion partners in prostate cancer. Mol Oncol 2023; 17:993-1006. [PMID: 37300660 DOI: 10.1002/1878-0261.13428] [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: 10/28/2022] [Revised: 02/26/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023] Open
Abstract
Genetic rearrangements that fuse an androgen-regulated promoter area with a protein-coding portion of an originally androgen-unaffected gene are frequent in prostate cancer, with the fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2-ERG fusion) being the most prevalent. Conventional hybridization- or amplification-based methods can test for the presence of expected gene fusions, but the exploratory analysis of currently unknown fusion partners is often cost-prohibitive. Here, we developed an innovative next-generation sequencing (NGS)-based approach for gene fusion analysis termed fusion sequencing via terminator-assisted synthesis (FTAS-seq). FTAS-seq can be used to enrich the gene of interest while simultaneously profiling the whole spectrum of its 3'-terminal fusion partners. Using this novel semi-targeted RNA-sequencing technique, we were able to identify 11 previously uncharacterized TMPRSS2 fusion partners and capture a range of TMPRSS2-ERG isoforms. We tested the performance of FTAS-seq with well-characterized prostate cancer cell lines and utilized the technique for the analysis of patient RNA samples. FTAS-seq chemistry combined with appropriate primer panels holds great potential as a tool for biomarker discovery that can support the development of personalized cancer therapies.
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Affiliation(s)
| | | | | | | | | | - Sonata Jarmalaitė
- National Cancer Institute, Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, Vilnius, Lithuania
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10
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Rago V, Di Agostino S. Novel Insights into the Role of the Antioxidants in Prostate Pathology. Antioxidants (Basel) 2023; 12:antiox12020289. [PMID: 36829848 PMCID: PMC9951863 DOI: 10.3390/antiox12020289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
To date, it is known that antioxidants protect cells from damage caused by oxidative stress and associated with pathological conditions. Several studies have established that inflammation is a state that anticipates the neoplastic transformation of the prostate. Although many experimental and clinical data have indicated the efficacy of antioxidants in preventing this form of cancer, the discrepant results, especially from recent large-scale randomized clinical trials, make it difficult to establish a real role for antioxidants in prostate tumor. Despite these concerns, clinical efficacy and safety data show that some antioxidants still hold promise for prostate cancer chemoprevention. Although more studies are needed, in this review, we briefly describe the most common antioxidants that have shown benefits in preclinical and clinical settings, focusing our attention on synthesizing the advances made so far in prostate cancer chemoprevention using antioxidants as interesting molecules for the challenges of future therapies.
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Affiliation(s)
- Vittoria Rago
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
- Correspondence: (V.R.); (S.D.A.); Tel.: +39-0984-493005 (V.R.); Fax: +39-0984-493271 (V.R.)
| | - Silvia Di Agostino
- Department of Health Sciences, Magna Græcia University of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (V.R.); (S.D.A.); Tel.: +39-0984-493005 (V.R.); Fax: +39-0984-493271 (V.R.)
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11
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Dathathri E, Isebia KT, Abali F, Lolkema MP, Martens JWM, Terstappen LWMM, Bansal R. Liquid Biopsy Based Circulating Biomarkers in Metastatic Prostate Cancer. Front Oncol 2022; 12:863472. [PMID: 35669415 PMCID: PMC9165750 DOI: 10.3389/fonc.2022.863472] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer is the most dominant male malignancy worldwide. The clinical presentation of prostate cancer ranges from localized indolent to rapidly progressing lethal metastatic disease. Despite a decline in death rate over the past years, with the advent of early diagnosis and new treatment options, challenges remain towards the management of metastatic prostate cancer, particularly metastatic castration sensitive prostate cancer (mCSPC) and castration resistant prostate cancer (mCRPC). Current treatments involve a combination of chemotherapy with androgen deprivation therapy and/or androgen receptor signalling inhibitors. However, treatment outcomes are heterogeneous due to significant tumor heterogeneity indicating a need for better prognostic biomarkers to identify patients with poor outcomes. Liquid biopsy has opened a plethora of opportunities from early diagnosis to (personalized) therapeutic disease interventions. In this review, we first provide recent insights about (metastatic) prostate cancer and its current treatment landscape. We highlight recent studies involving various circulating biomarkers such as circulating tumor cells, genetic markers, circulating nucleic acids, extracellular vesicles, tumor-educated platelets, and the secretome from (circulating) tumor cells and tumor microenvironment in metastatic prostate cancer. The comprehensive array of biomarkers can provide a powerful approach to understanding the spectrum of prostate cancer disease and guide in developing improved and personalized treatments for patients.
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Affiliation(s)
- Eshwari Dathathri
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Khrystany T. Isebia
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - Fikri Abali
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Martijn P. Lolkema
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - John W. M. Martens
- Erasmus Medical Center Cancer Institute, University Medical Center Rotterdam, Department of Medical Oncology, Rotterdam, Netherlands
| | - Leon W. M. M. Terstappen
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
| | - Ruchi Bansal
- Department of Medical Cell BioPhysics, Faculty of Science and Technology, Technical Medical Center, University of Twente, Enschede, Netherlands
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12
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Khosh Kish E, Choudhry M, Gamallat Y, Buharideen SM, D D, Bismar TA. The Expression of Proto-Oncogene ETS-Related Gene ( ERG) Plays a Central Role in the Oncogenic Mechanism Involved in the Development and Progression of Prostate Cancer. Int J Mol Sci 2022; 23:ijms23094772. [PMID: 35563163 PMCID: PMC9105369 DOI: 10.3390/ijms23094772] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/17/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
The ETS-related gene (ERG) is proto-oncogene that is classified as a member of the ETS transcription factor family, which has been found to be consistently overexpressed in about half of the patients with clinically significant prostate cancer (PCa). The overexpression of ERG can mostly be attributed to the fusion of the ERG and transmembrane serine protease 2 (TMPRSS2) genes, and this fusion is estimated to represent about 85% of all gene fusions observed in prostate cancer. Clinically, individuals with ERG gene fusion are mostly documented to have advanced tumor stages, increased mortality, and higher rates of metastasis in non-surgical cohorts. In the current review, we elucidate ERG’s molecular interaction with downstream genes and the pathways associated with PCa. Studies have documented that ERG plays a central role in PCa progression due to its ability to enhance tumor growth by promoting inflammatory and angiogenic responses. ERG has also been implicated in the epithelial–mesenchymal transition (EMT) in PCa cells, which increases the ability of cancer cells to metastasize. In vivo, research has demonstrated that higher levels of ERG expression are involved with nuclear pleomorphism that prompts hyperplasia and the loss of cell polarity.
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Affiliation(s)
- Ealia Khosh Kish
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2V 1P9, Canada; (E.K.K.); (M.C.); (Y.G.); (S.M.B.); (D.D.)
| | - Muhammad Choudhry
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2V 1P9, Canada; (E.K.K.); (M.C.); (Y.G.); (S.M.B.); (D.D.)
| | - Yaser Gamallat
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2V 1P9, Canada; (E.K.K.); (M.C.); (Y.G.); (S.M.B.); (D.D.)
- Alberta Precision Laboratories, Calgary, AB T2V 1P9, Canada
| | - Sabrina Marsha Buharideen
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2V 1P9, Canada; (E.K.K.); (M.C.); (Y.G.); (S.M.B.); (D.D.)
- Alberta Precision Laboratories, Calgary, AB T2V 1P9, Canada
| | - Dhananjaya D
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2V 1P9, Canada; (E.K.K.); (M.C.); (Y.G.); (S.M.B.); (D.D.)
- Alberta Precision Laboratories, Calgary, AB T2V 1P9, Canada
| | - Tarek A. Bismar
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2V 1P9, Canada; (E.K.K.); (M.C.); (Y.G.); (S.M.B.); (D.D.)
- Alberta Precision Laboratories, Calgary, AB T2V 1P9, Canada
- Departments of Oncology, Biochemistry and Molecular Biology, Calgary, AB T2V 1P9, Canada
- Tom Baker Cancer Center, Arnie Charbonneau Cancer Institute, Calgary, AB T2V 1P9, Canada
- Correspondence: ; Tel.: +1-403-943-8430; Fax: +1-403-943-3333
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13
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Gockel LM, Pfeifer V, Baltes F, Bachmaier RD, Wagner KG, Bendas G, Gütschow M, Sosič I, Steinebach C. Design, synthesis, and characterization of PROTACs targeting the androgen receptor in prostate and lung cancer models. Arch Pharm (Weinheim) 2022; 355:e2100467. [PMID: 35128717 DOI: 10.1002/ardp.202100467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023]
Abstract
Although the androgen receptor (AR) is a validated target for the treatment of prostate cancer, resistance to antiandrogens necessitates the development of new therapeutic modalities. Exploiting the ubiquitin-proteasome system with proteolysis-targeting chimeras (PROTACs) has become a practical approach to degrade specific proteins and thus to extend the portfolio of small molecules used for the treatment of a broader spectrum of diseases. Herein, we present three subgroups of enzalutamide-based PROTACs in which only the exit vector was modified. By recruiting cereblon, we were able to demonstrate the potent degradation of AR in lung cancer cells. Furthermore, the initial evaluation enabled the design of an optimized PROTAC with a rigid linker that degraded AR with a DC50 value in the nanomolar range. These results provide novel AR-directed PROTACs and a clear rationale for further investigating AR involvement in lung cancer models.
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Affiliation(s)
- Lukas M Gockel
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Vladlena Pfeifer
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Fabian Baltes
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Rafael D Bachmaier
- Department of Pharmaceutical Technology, Pharmaceutical Institute, Bonn, Germany
| | - Karl G Wagner
- Department of Pharmaceutical Technology, Pharmaceutical Institute, Bonn, Germany
| | - Gerd Bendas
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Michael Gütschow
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, Bonn, Germany
| | - Izidor Sosič
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Christian Steinebach
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, Bonn, Germany
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14
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CaV1.3 enhanced store operated calcium promotes resistance to androgen deprivation in prostate cancer. Cell Calcium 2022; 103:102554. [DOI: 10.1016/j.ceca.2022.102554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/24/2022] [Accepted: 02/06/2022] [Indexed: 01/01/2023]
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15
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Chaves LP, Melo CM, Saggioro FP, dos Reis RB, Squire JA. Epithelial-Mesenchymal Transition Signaling and Prostate Cancer Stem Cells: Emerging Biomarkers and Opportunities for Precision Therapeutics. Genes (Basel) 2021; 12:1900. [PMID: 34946849 PMCID: PMC8701270 DOI: 10.3390/genes12121900] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022] Open
Abstract
Prostate cancers may reactivate a latent embryonic program called the epithelial-mesenchymal transition (EMT) during the development of metastatic disease. Through EMT, tumors can develop a mesenchymal phenotype similar to cancer stem cell traits that contributes to metastasis and variation in therapeutic responses. Some of the recurrent somatic mutations of prostate cancer affect EMT driver genes and effector transcription factors that induce the chromatin- and androgen-dependent epigenetic alterations that characterize castrate-resistant prostate cancer (CRPC). EMT regulators in prostate cancer comprise transcription factors (SNAI1/2, ZEB1, TWIST1, and ETS), tumor suppressor genes (RB1, PTEN, and TP53), and post-transcriptional regulators (miRNAs) that under the selective pressures of antiandrogen therapy can develop an androgen-independent metastatic phenotype. In prostate cancer mouse models of EMT, Slug expression, as well as WNT/β-Catenin and notch signaling pathways, have been shown to increase stemness potential. Recent single-cell transcriptomic studies also suggest that the stemness phenotype of advanced prostate cancer may be related to EMT. Other evidence correlates EMT and stemness with immune evasion, for example, activation of the polycomb repressor complex I, promoting EMT and stemness and cytokine secretion through RB1, TP53, and PRC1. These findings are helping clinical trials in CRPC that seek to understand how drugs and biomarkers related to the acquisition of EMT can improve drug response.
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Affiliation(s)
- Luiz Paulo Chaves
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (L.P.C.); (C.M.M.)
| | - Camila Morais Melo
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (L.P.C.); (C.M.M.)
| | - Fabiano Pinto Saggioro
- Pathology Department, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil;
| | - Rodolfo Borges dos Reis
- Division of Urology, Department of Surgery and Anatomy, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil;
| | - Jeremy Andrew Squire
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14048-900, SP, Brazil; (L.P.C.); (C.M.M.)
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
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16
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Morgan R, da Silveira WA, Kelly RC, Overton I, Allott EH, Hardiman G. Long non-coding RNAs and their potential impact on diagnosis, prognosis, and therapy in prostate cancer: racial, ethnic, and geographical considerations. Expert Rev Mol Diagn 2021; 21:1257-1271. [PMID: 34666586 DOI: 10.1080/14737159.2021.1996227] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Advances in high-throughput sequencing have greatly advanced our understanding of long non-coding RNAs (lncRNAs) in a relatively short period of time. This has expanded our knowledge of cancer, particularly how lncRNAs drive many important cancer phenotypes via their regulation of gene expression. AREAS COVERED Men of African descent are disproportionately affected by PC in terms of incidence, morbidity, and mortality. LncRNAs could serve as biomarkers to differentiate low-risk from high-risk diseases. Additionally, they may represent therapeutic targets for advanced and castrate-resistant cancer. We review current research surrounding lncRNAs and their association with PC. We discuss how lncRNAs can provide new insights and diagnostic biomarkers for African American men. Finally, we review advances in computational approaches that predict the regulatory effects of lncRNAs in cancer. EXPERT OPINION PC diagnostic biomarkers that offer high specificity and sensitivity are urgently needed. PC specific lncRNAs are compelling as diagnostic biomarkers owing to their high tissue and tumor specificity and presence in bodily fluids. Recent studies indicate that PCA3 clinical utility might be restricted to men of European descent. Further work is required to develop lncRNA biomarkers tailored for men of African descent.
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Affiliation(s)
- Rebecca Morgan
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Willian Abraham da Silveira
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Ryan Christopher Kelly
- Faculty of Medicine, Health and Life Sciences, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ian Overton
- Faculty of Medicine, Health and Life Sciences, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emma H Allott
- Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK.,Faculty of Medicine, Health and Life Sciences, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.,Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Gary Hardiman
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK.,Department of Medicine, Medical University of South Carolina (MUSC), Charleston, South Carolina
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17
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Proteomic Landscape of Prostate Cancer: The View Provided by Quantitative Proteomics, Integrative Analyses, and Protein Interactomes. Cancers (Basel) 2021; 13:cancers13194829. [PMID: 34638309 PMCID: PMC8507874 DOI: 10.3390/cancers13194829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer is the second most frequent cancer of men worldwide. While the genetic landscapes and heterogeneity of prostate cancer are relatively well-known already, methodological developments now allow for studying basic and dynamic proteomes on a large scale and in a quantitative fashion. This aids in revealing the functional output of cancer genomes. It has become evident that not all aberrations at the genetic and transcriptional level are translated to the proteome. In addition, the proteomic level contains heterogeneity, which increases as the cancer progresses from primary prostate cancer (PCa) to metastatic and castration-resistant prostate cancer (CRPC). While multiple aspects of prostate adenocarcinoma proteomes have been studied, less is known about proteomes of neuroendocrine prostate cancer (NEPC). In this review, we summarize recent developments in prostate cancer proteomics, concentrating on the proteomic landscapes of clinical prostate cancer, cell line and mouse model proteomes interrogating prostate cancer-relevant signaling and alterations, and key prostate cancer regulator interactomes, such as those of the androgen receptor (AR). Compared to genomic and transcriptomic analyses, the view provided by proteomics brings forward changes in prostate cancer metabolism, post-transcriptional RNA regulation, and post-translational protein regulatory pathways, requiring the full attention of studies in the future.
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18
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Sigorski D, Gulczyński J, Sejda A, Rogowski W, Iżycka-Świeszewska E. Investigation of Neural Microenvironment in Prostate Cancer in Context of Neural Density, Perineural Invasion, and Neuroendocrine Profile of Tumors. Front Oncol 2021; 11:710899. [PMID: 34277455 PMCID: PMC8281889 DOI: 10.3389/fonc.2021.710899] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/21/2021] [Indexed: 12/20/2022] Open
Abstract
Background Cancer stroma contains the neural compartment with specific components and action. Neural microenvironment processing includes among others axonogenesis, perineural invasion (PNI), neurosignaling, and tumor cell neural/neuroendocrine differentiation. Growing data suggest that tumor-neural crosstalk plays an important function in prostate cancer (PCa) biology. However, the mechanisms involved in PNI and axonogenesis, as well as their patho-clinical correlations in this tumor are unclear. Methods The present study was carried out on FFPE samples of 73 PCa and 15 benign prostate (BP) cases. Immunohistochemistry with neural markers PGP9.5, TH, and NFP was performed on constructed TMAs and selected tissue sections. The analyzed parameters of tumor innervation included small nerve density (ND) measured on pan-neural marker (PGP9.5) and TH s4tained slides, as well assessment of PNI presence and morphology. The qualitative and topographic aspects were studied. In addition, the expression of neuroendocrine marker chromogranin and NPY was assessed with dedicated indexes. The correlations of the above parameters with basic patho-clinical data such as patients’ age, tumor stage, grade, angioinvasion, and ERG status were examined. Results The study showed that innervation parameters differed between cancer and BP. The neural network in PCa revealed heterogeneity, and ND PGP9.5 in tumor was significantly lower than in its periphery. The density of sympathetic TH-positive fibers and its proportion to all fibers was lower in cancer than in the periphery and BP samples. Perineural invasion was confirmed in 76% of cases, usually multifocally, occurring more commonly in tumors with a higher grade. NPY expression in PCa cells was common with its intensity often rising towards PNI. ERG+ tumors showed higher ND, more frequent PNI, and a higher stage. Moreover, chromogranin-positive cells were more pronounced in PCa with higher NPY expression. Conclusions The analysis showed an irregular axonal network in prostate cancer with higher neural density (panneural and adrenergic) in the surroundings and the invasive front. ND and PNI interrelated with NPY expression, neuroendocrine differentiation, and ERG status. The above findings support new evidence for the presence of autocrine and paracrine interactions in prostate cancer neural microenvironment.
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Affiliation(s)
- Dawid Sigorski
- Department of Oncology, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland.,Department of Oncology and Immuno-Oncology, Warmian-Masurian Cancer Center of the Ministry of the Interior and Administration Hospital, Olsztyn, Poland
| | - Jacek Gulczyński
- Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland.,Department of Pathomorphology, Copernicus Hospital, Gdańsk, Poland
| | - Aleksandra Sejda
- Department of Pathomorphology, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Wojciech Rogowski
- Department of Health, Pomeranian University in Słupsk, Słupsk, Poland.,Department of Oncology, Chemotherapy, Clinical trials, Regional Hospital, Słupsk, Poland
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland.,Department of Pathomorphology, Copernicus Hospital, Gdańsk, Poland
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