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Ordulu Z, Watkins J, Ritterhouse LL. Molecular Pathology of Ovarian Epithelial Neoplasms: Predictive, Prognostic, and Emerging Biomarkers. Clin Lab Med 2024; 44:199-219. [PMID: 38821641 DOI: 10.1016/j.cll.2023.08.004] [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] [Indexed: 06/02/2024]
Abstract
This review focuses on the diagnostic, prognostic, and predictive molecular biomarkers in ovarian epithelial neoplasms in the context of their morphologic classifications. Currently, most clinically actionable molecular findings are reported in high-grade serous carcinomas; however, the data on less common tumor types are rapidly accelerating. Overall, the advances in genomic knowledge over the last decade highlight the significance of integrating molecular findings with morphology in ovarian epithelial tumors for a wide-range of clinical applications, from assistance in diagnosis to predicting response to therapy.
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Affiliation(s)
- Zehra Ordulu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA
| | - Jaclyn Watkins
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA
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2
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Davidson B, Holth A, Lindemann K, Zahl Eriksson AG, Nilsen TA, Torgunrud A. Molecular characteristics of tubo-ovarian carcinosarcoma at different anatomic locations. Virchows Arch 2024:10.1007/s00428-024-03821-9. [PMID: 38733380 DOI: 10.1007/s00428-024-03821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/23/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Carcinosarcoma (CS) is an uncommon and clinically aggressive malignancy. The objective of the present study was to characterize the molecular features of CS at various anatomic locations, including serous effusions. Specimens (n = 32) consisted of 25 biopsies/surgical resection specimens and 7 serous effusions (6 peritoneal, 1 pleural) from 25 patients. Fresh-frozen cell pellets and surgical specimens underwent targeted next-generation sequencing covering 50 unique genes. A total of 31 mutations were found in 25 of the 32 tumors studied, of which 1 had 3 mutations, 4 had 2 different mutations, and 20 had a single mutation. The most common mutations were in TP53 (n = 25 in 24 tumors; 1 tumor with 2 different mutations), with less common mutations found in RB1 (n = 2), MET (n = 1), KRAS (n = 1), PTEN (n = 1), and KIT (n = 1). Patient-matched specimens harbored the same TP53 mutation. Tumors with no detected mutations were more common in serous effusion specimens (3/7; 43%) compared with surgical specimens (4/25; 16%). In conclusion, the molecular landscape of CS is dominated by TP53 mutations, reinforcing the observation that the majority of these tumors develop from high-grade serous carcinoma. Whether CS cells in serous effusions differ from their counterparts in solid lesions remains uncertain.
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Affiliation(s)
- Ben Davidson
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway.
- Faculty of Medicine, University of Oslo, Institute of Clinical Medicine, N-0316, Oslo, Norway.
| | - Arild Holth
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Kristina Lindemann
- Faculty of Medicine, University of Oslo, Institute of Clinical Medicine, N-0316, Oslo, Norway
- Department of Gynecologic Oncology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Ane Gerda Zahl Eriksson
- Faculty of Medicine, University of Oslo, Institute of Clinical Medicine, N-0316, Oslo, Norway
- Department of Gynecologic Oncology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Thale Andrea Nilsen
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
| | - Annette Torgunrud
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Montebello, N-0310, Oslo, Norway
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Tang LS, Zhou YW, Wang JL, Zhang GX, Xu CH, Liu JY, Qiu M. Epidemiology, site-specific characteristics and survival of carcinosarcoma: a retrospective study based on SEER database. BMJ Open 2023; 13:e077974. [PMID: 38101828 PMCID: PMC10729011 DOI: 10.1136/bmjopen-2023-077974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
OBJECTIVES Carcinosarcoma (CS) is a rare and biphasic malignancy characterised by a highly invasive biological nature and poor prognosis. This study explored the epidemiology, site-specific characteristics and survival outcome of CS. DESIGN We conducted a retrospective study in the Surveillance, Epidemiology and End Results (SEER) database (1975-2018) for primary CS. SETTING AND PARTICIPANTS SEER database includes publicly available information from regional and state cancer registries in the US centres. A total of 5042 CS patients were identified. We selected the top five anatomic CS (uterus, double adnexa, lung, bladder and breast) patients for further analysis. PRIMARY OUTCOME MEASURES Incidence was estimated by geographical region, age, sex, race, stage and primary site. Trends were calculated using joinpoint regression. The cancer-specific survival (CSS) rate and initial treatment were summarised. RESULTS Nearly 80% of CS occurred in the uterus and double adnexa, followed by lung, bladder and breast. The elderly and black population presented the highest age-adjusted rate of CS. The rates of distant metastasis in CS progressively increased from 1989 to 2018. Atlanta was the area with the highest incidence at 0.7 per 100 000. Pulmonary and bladder CS more frequently occurred in men and were diagnosed with regional stage. Distant metastasis was mostly found in ovary/fallopian tube CS. Radiotherapy was more commonly applied in uterine CS, while adnexa CS cases were more likely to receive chemotherapy. Multiple treatments were more used in breast CS. Pulmonary CS seemed to suffer worse CSS (median: 9.92 months), for which radiotherapy might not provide survival benefits (HR 0.60, 95% CI 0.42 to 0.86). Compared with the common histological types in each site, CS had the shortest survival. CONCLUSIONS CS has unique clinical features in each primary site. Substantial prognosis variances exist based on tumour locations. The aggressive course is the common feature in CS at all sites.
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Affiliation(s)
- Lian-Sha Tang
- West China Hospital of Sichuan University, Chengdu, China
| | - Yu-Wen Zhou
- Department of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Jia-Ling Wang
- West China Hospital of Sichuan University, Chengdu, China
| | - Guo-Xu Zhang
- West China Hospital of Sichuan University, Chengdu, China
| | - Chen-Hao Xu
- West China Hospital of Sichuan University, Chengdu, China
| | - Ji-Yan Liu
- Department of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Meng Qiu
- Department of Abdominal Oncology, West China Hospital of Sichuan University, Chengdu, China
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Ramphal K, Hadfield MJ, Bandera CM, Hart J, Dizon DS. Genomic and Molecular Characteristics of Ovarian Carcinosarcoma. Am J Clin Oncol 2023; 46:572-576. [PMID: 37986208 DOI: 10.1097/coc.0000000000001056] [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: 11/22/2023]
Abstract
Ovarian carcinosarcoma (OCS) is a rare malignancy with a poor prognosis. It is a biphasic tumor with malignant epithelial and mesenchymal components. A few mutations commonly seen in cancer have been identified in OCS, including TP53, PIK3CA, c-myc, ZNF217, ARID1A, and CTNNB1. Some OCS tumors have shown vascular endothelial growth factor positivity and limited HER2 expression. There is evidence of homologous recombination deficiency in OCS. This malignancy can be categorized as copy number high but has not been shown to have a high tumor mutational burden. There are mixed findings regarding the presence of biomarkers targeted by immune checkpoint inhibitors in OCS. For treatments other than systemic chemotherapy, the data available are largely based on in vitro and in vivo studies. In addition, there are case reports citing the use of poly-ADP ribose polymerase inhibitors, vascular endothelial growth factor inhibitors, and immunotherapy with varying degrees of success. This review paper will discuss the molecular and genomic characteristics of OCS, which can guide future treatment strategies.
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Affiliation(s)
- Kristy Ramphal
- Warren Alpert Medical School of Brown University, Legorreta Cancer Center, Providence, RI
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Erdogan EG, Yalta TD, Can N, Süt N, Taştekin E, Usta U, Puyan FÖ, Usturalı Keskin FE, Kurt BB. Clinicopathological and molecular analyses of uterine carcinosarcomas using next-generation sequencing: A single-center experience. INDIAN J PATHOL MICR 2023; 66:449-455. [PMID: 37530323 DOI: 10.4103/ijpm.ijpm_777_21] [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] [Indexed: 08/03/2023] Open
Abstract
Background Uterine carcinosarcomas (UCS) constitute 3-4% of all uterine malignancies and 16% of deaths caused due to uterine neoplasms. Aim In this study, we aimed to perform DNA-based mutation analysis in 12 genes (KRAS, NRAS, EGFR, C-KIT, BRAF, PDGFRA, ALK, ERBB2, ERBB3, ESR1, RAF1, PIK3CA) to determine the molecular subtypes of UCS using next-generation sequencing (NGS) in patients with aggressive UCS and poor prognosis. We aimed to compare the results of our analysis with clinicopathological data to contribute to the development of targeted therapy approaches related to the molecular changes of UCS. Materials and Methods In this study, we included 12 cases diagnosed with uterine carcinosarcomas and examined the changes in oncogenes that play a role in UCS pathogenesis. For the analysis of mutation, the clinicopathological data were compared with the variations in the DNA-based gene panel consisting of 12 genes and 1237 variants in the UCS using the NGS method. Results EGFR mutation was found in 91.7% of the cases, mutation in 41.7%, PDGFRA mutation in 25%, KRAS and PIK3CA mutation in 16.7%, and C-KIT mutation in 8.3% of the cases. Although no statistical significance was found between the detected mutation and clinicopathological data, it was concluded that PDGFRA mutation might be associated with advanced-stage disease development. Conclusion This study's findings regarding different molecular types of UCS and information on oncogenesis of UCS can provide inferences for targeted therapies in the future by identifying targetable mutations representing early oncogenic events and thereby contribute toward further studies on this subject.
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Affiliation(s)
- Ezgi Genc Erdogan
- Department of Pathology, Faculty of Medicine, Trakya University, Edirne; Department of Pathology, Lüleburgaz State Hospital, Kırklareli, Turkey
| | - Tülin D Yalta
- Department of Pathology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Nuray Can
- Department of Pathology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Necdet Süt
- Department of Biostatistics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Ebru Taştekin
- Department of Pathology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Ufuk Usta
- Department of Pathology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Fulya Öz Puyan
- Department of Pathology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | | | - Busem B Kurt
- Department of Pathology, Tekirdağ State Hospital, Tekirdağ, Turkey
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Di Fiore R, Suleiman S, Drago-Ferrante R, Subbannayya Y, Suleiman S, Vasileva-Slaveva M, Yordanov A, Pentimalli F, Giordano A, Calleja-Agius J. The Role of FBXW7 in Gynecologic Malignancies. Cells 2023; 12:1415. [PMID: 37408248 DOI: 10.3390/cells12101415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 07/07/2023] Open
Abstract
The F-Box and WD Repeat Domain Containing 7 (FBXW7) protein has been shown to regulate cellular growth and act as a tumor suppressor. This protein, also known as FBW7, hCDC4, SEL10 or hAGO, is encoded by the gene FBXW7. It is a crucial component of the Skp1-Cullin1-F-box (SCF) complex, which is a ubiquitin ligase. This complex aids in the degradation of many oncoproteins, such as cyclin E, c-JUN, c-MYC, NOTCH, and MCL1, via the ubiquitin-proteasome system (UPS). The FBXW7 gene is commonly mutated or deleted in numerous types of cancer, including gynecologic cancers (GCs). Such FBXW7 mutations are linked to a poor prognosis due to increased treatment resistance. Hence, detection of the FBXW7 mutation may possibly be an appropriate diagnostic and prognostic biomarker that plays a central role in determining suitable individualized management. Recent studies also suggest that, under specific circumstances, FBXW7 may act as an oncogene. There is mounting evidence indicating that the aberrant expression of FBXW7 is involved in the development of GCs. The aim of this review is to give an update on the role of FBXW7 as a potential biomarker and also as a therapeutic target for novel treatments, particularly in the management of GCs.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta
| | | | - Yashwanth Subbannayya
- School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Sarah Suleiman
- Whipps Cross Hospital, Barts Health NHS Trust, Leytonstone, London E11 1NR, UK
| | - Mariela Vasileva-Slaveva
- Department of Breast Surgery, "Dr. Shterev" Hospital, 1330 Sofia, Bulgaria
- Research Institute, Medical University Pleven, 5800 Pleven, Bulgaria
- Bulgarian Breast and Gynecological Cancer Association, 1784 Sofia, Bulgaria
| | - Angel Yordanov
- Department of Gynecological Oncology, Medical University Pleven, 5800 Pleven, Bulgaria
| | - Francesca Pentimalli
- Department of Medicine and Surgery, LUM University "Giuseppe DeGennaro", 70010 Casamassima, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta
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Ordulu Z, Watkins J, Ritterhouse LL. Molecular Pathology of Ovarian Epithelial Neoplasms: Predictive, Prognostic, and Emerging Biomarkers. Surg Pathol Clin 2021; 14:415-428. [PMID: 34373093 DOI: 10.1016/j.path.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This review focuses on the diagnostic, prognostic, and predictive molecular biomarkers in ovarian epithelial neoplasms in the context of their morphologic classifications. Currently, most clinically actionable molecular findings are reported in high-grade serous carcinomas; however, the data on less common tumor types are rapidly accelerating. Overall, the advances in genomic knowledge over the last decade highlight the significance of integrating molecular findings with morphology in ovarian epithelial tumors for a wide-range of clinical applications, from assistance in diagnosis to predicting response to therapy.
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Affiliation(s)
- Zehra Ordulu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA
| | - Jaclyn Watkins
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA.
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8
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Di Fiore R, Suleiman S, Pentimalli F, O’Toole SA, O’Leary JJ, Ward MP, Conlon NT, Sabol M, Ozretić P, Erson-Bensan AE, Reed N, Giordano A, Herrington CS, Calleja-Agius J. Could MicroRNAs Be Useful Tools to Improve the Diagnosis and Treatment of Rare Gynecological Cancers? A Brief Overview. Int J Mol Sci 2021; 22:ijms22083822. [PMID: 33917022 PMCID: PMC8067678 DOI: 10.3390/ijms22083822] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
Gynecological cancers pose an important public health issue, with a high incidence among women of all ages. Gynecological cancers such as malignant germ-cell tumors, sex-cord-stromal tumors, uterine sarcomas and carcinosarcomas, gestational trophoblastic neoplasia, vulvar carcinoma and melanoma of the female genital tract, are defined as rare with an annual incidence of <6 per 100,000 women. Rare gynecological cancers (RGCs) are associated with poor prognosis, and given the low incidence of each entity, there is the risk of delayed diagnosis due to clinical inexperience and limited therapeutic options. There has been a growing interest in the field of microRNAs (miRNAs), a class of small non-coding RNAs of ∼22 nucleotides in length, because of their potential to regulate diverse biological processes. miRNAs usually induce mRNA degradation and translational repression by interacting with the 3' untranslated region (3'-UTR) of target mRNAs, as well as other regions and gene promoters, as well as activating translation or regulating transcription under certain conditions. Recent research has revealed the enormous promise of miRNAs for improving the diagnosis, therapy and prognosis of all major gynecological cancers. However, to date, only a few studies have been performed on RGCs. In this review, we summarize the data currently available regarding RGCs.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Correspondence: (R.D.F.); (J.C.-A.); Tel.: +356-2340-3871 (R.D.F.); +356-2340-1892 (J.C.-A.)
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Napoli, Italy;
| | - Sharon A. O’Toole
- Departments of Obstetrics and Gynaecology and Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, 8 Dublin, Ireland;
| | - John J. O’Leary
- Department of Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, 8 Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - Mark P. Ward
- Department of Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, 8 Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - Neil T. Conlon
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, 9 Dublin, Ireland;
| | - Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.S.); (P.O.)
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.S.); (P.O.)
| | - Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University, Ankara 06810, Turkey;
| | - Nicholas Reed
- Beatson Oncology Centre, Gartnavel General Hospital, 1053 Great Western Road, Glasgow G12 0YN, UK;
| | - Antonio Giordano
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - C. Simon Herrington
- Cancer Research UK Edinburgh Centre, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK;
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Correspondence: (R.D.F.); (J.C.-A.); Tel.: +356-2340-3871 (R.D.F.); +356-2340-1892 (J.C.-A.)
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Brunetti M, Panagopoulos I, Kostolomov I, Davidson B, Heim S, Micci F. Mutation analysis and genomic imbalances of cells found in effusion fluids from patients with ovarian cancer. Oncol Lett 2020; 20:2273-2279. [PMID: 32782545 PMCID: PMC7400987 DOI: 10.3892/ol.2020.11782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/29/2020] [Indexed: 01/02/2023] Open
Abstract
Ovarian carcinomas and carcinosarcomas often cause malignant effusions, an accumulation within serous cavities of fluid containing cancer cells. Few studies have focused on the molecular alterations and genetic mechanisms behind effusion formation. The present study investigated the mutation status of TP53, PIK3CA, KRAS, HRAS, NRAS and BRAF in effusion fluids from 103 patients with ovarian cancer. In addition, array Comparative Genomic Hybridization (aCGH) analysis was performed on 20 effusions from patients with high-grade serous carcinoma (10 cases positive for TP53 mutation and 10 with TP53 wild-type). TP53 mutations, two of which were novel: c.826_830delCCTGT and c.475_476GC>TT, were identified in 44% of the cases. Mutations in KRAS, HRAS, and PIK3CA were identified in two, two and four cases, respectively. None of the effusions analysed showed NRAS or BRAF mutations. The aCGH analysis revealed highly imbalanced genomes similar to those described in primary ovarian carcinomas. No specific profile was indicated to distinguish tumors with TP53 mutations from those without. The molecular profiling of cells found in effusion fluids from patients with ovarian cancer thus showed considerable molecular heterogeneity. TP53 seems to be the most frequently mutated gene in these cells and may serve a leading role in the metastatic process.
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Affiliation(s)
- Marta Brunetti
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway.,Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway
| | - Ilyá Kostolomov
- Section for Applied Informatics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway
| | - Ben Davidson
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0424 Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway
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Chen X, Wan L, Wang W, Xi WJ, Yang AG, Wang T. Re-recognition of pseudogenes: From molecular to clinical applications. Theranostics 2020; 10:1479-1499. [PMID: 32042317 PMCID: PMC6993246 DOI: 10.7150/thno.40659] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudogenes were initially regarded as "nonfunctional" genomic elements that did not have protein-coding abilities due to several endogenous inactivating mutations. Although pseudogenes are widely expressed in prokaryotes and eukaryotes, for decades, they have been largely ignored and classified as gene "junk" or "relics". With the widespread availability of high-throughput sequencing analysis, especially omics technologies, knowledge concerning pseudogenes has substantially increased. Pseudogenes are evolutionarily conserved and derive primarily from a mutation or retrotransposon, conferring the pseudogene with a "gene repository" role to store and expand genetic information. In contrast to previous notions, pseudogenes have a variety of functions at the DNA, RNA and protein levels for broadly participating in gene regulation to influence the development and progression of certain diseases, especially cancer. Indeed, some pseudogenes have been proven to encode proteins, strongly contradicting their "trash" identification, and have been confirmed to have tissue-specific and disease subtype-specific expression, indicating their own value in disease diagnosis. Moreover, pseudogenes have been correlated with the life expectancy of patients and exhibit great potential for future use in disease treatment, suggesting that they are promising biomarkers and therapeutic targets for clinical applications. In this review, we summarize the natural properties, functions, disease involvement and clinical value of pseudogenes. Although our knowledge of pseudogenes remains nascent, this field deserves more attention and deeper exploration.
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