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Li J, Chen Z, Xiao W, Liang H, Liu Y, Hao W, Zhang Y, Wei F. Chromosome instability region analysis and identification of the driver genes of the epithelial ovarian cancer cell lines A2780 and SKOV3. J Cell Mol Med 2023; 27:3259-3270. [PMID: 37525498 PMCID: PMC10623538 DOI: 10.1111/jcmm.17893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the most prevalent gynaecological cancers worldwide. The molecular mechanisms of serous ovarian cancer (SOC) remain unclear and not well understood. SOC cases are primarily diagnosed at the late stage, resulting in a poor prognosis. Advances in molecular biology techniques allow us to obtain a better understanding of precise molecular mechanisms and to identify the chromosome instability region and key driver genes in the carcinogenesis and progression of SOC. Whole-exome sequencing was performed on the normal ovarian cell line IOSE80 and the EOC cell lines SKOV3 and A2780. The single-nucleotide variation burden, distribution, frequency and signature followed the known ovarian mutation profiles, without chromosomal bias. Recurrently mutated ovarian cancer driver genes, including LRP1B, KMT2A, ARID1A, KMT2C and ATRX were also found in two cell lines. The genome distribution of copy number alterations was found by copy number variation (CNV) analysis, including amplification of 17q12 and 4p16.1 and deletion of 10q23.33. The CNVs of MED1, GRB7 and MIEN1 located at 17q12 were found to be correlated with the overall survival of SOC patients (MED1: p = 0.028, GRB7: p = 0.0048, MIEN1: p = 0.0051), and the expression of the three driver genes in the ovarian cell line IOSE80 and EOC cell lines SKOV3 and A2780 was confirmed by western blot and cell immunohistochemistry.
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Affiliation(s)
- Jianxiong Li
- Department of GynecologyLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Zexin Chen
- Department of Cell Biology and Medical Genetics, School of Basic Medical SciencesGuangdong Pharmaceutical UniversityGuangzhouChina
| | - Wentao Xiao
- Department of GynecologyLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Huaguo Liang
- Department of Cell Biology and Medical Genetics, School of Basic Medical SciencesGuangdong Pharmaceutical UniversityGuangzhouChina
| | - Yanan Liu
- The Genetics LaboratoryLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Wenqi Hao
- The Genetics LaboratoryLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
| | - Yongli Zhang
- Department of Cell Biology and Medical Genetics, School of Basic Medical SciencesGuangdong Pharmaceutical UniversityGuangzhouChina
| | - Fengxiang Wei
- The Genetics LaboratoryLonggang District Maternity and Child Healthcare Hospital of Shenzhen City (Longgang Maternity and Child Institute of Shantou University Medical College)ShenzhenChina
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2
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Torkildsen CF, Thomsen LCV, Sande RK, Krakstad C, Stefansson I, Lamark EK, Knappskog S, Bjørge L. Molecular and phenotypic characteristics influencing the degree of cytoreduction in high-grade serous ovarian carcinomas. Cancer Med 2023. [PMID: 37191035 DOI: 10.1002/cam4.6085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND High-grade serous ovarian carcinoma (HGSOC) is the deadliest ovarian cancer subtype, and survival relates to initial cytoreductive surgical treatment. The existing tools for surgical outcome prediction remain inadequate for anticipating the outcomes of the complex relationship between tumour biology, clinical phenotypes, co-morbidity and surgical skills. In this genotype-phenotype association study, we combine phenotypic markers with targeted DNA sequencing to discover novel biomarkers to guide the surgical management of primary HGSOC. METHODS Primary tumour tissue samples (n = 97) and matched blood from a phenotypically well-characterised treatment-naïve HGSOC patient cohort were analysed by targeted massive parallel DNA sequencing (next generation sequencing [NGS]) of a panel of 360 cancer-related genes. Association analyses were performed on phenotypic traits related to complete cytoreductive surgery, while logistic regression analysis was applied for the predictive model. RESULTS The positive influence of complete cytoreductive surgery (R0) on overall survival was confirmed (p = 0.003). Before surgery, low volumes of ascitic fluid, lower CA125 levels, higher platelet counts and relatively lower clinical stage at diagnosis were all indicators, alone and combined, for complete cytoreduction (R0). Mutations in either the chromatin remodelling SWI_SNF (p = 0.036) pathway or the histone H3K4 methylation pathway (p = 0.034) correlated with R0. The R0 group also demonstrated higher tumour mutational burden levels (p = 0.028). A predictive model was developed by combining two phenotypes and the mutational status of five genes and one genetic pathway, enabling the prediction of surgical outcomes in 87.6% of the cases in this cohort. CONCLUSION Inclusion of molecular biomarkers adds value to the pre-operative stratification of HGSOC patients. A potential preoperative risk stratification model combining phenotypic traits and single-gene mutational status is suggested, but the set-up needs to be validated in larger cohorts.
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Affiliation(s)
- Cecilie Fredvik Torkildsen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
| | - Liv Cecilie Vestrheim Thomsen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Ragnar Kvie Sande
- Department of Obstetrics and Gynecology, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Camilla Krakstad
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Ingunn Stefansson
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Eva Karin Lamark
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Line Bjørge
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
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3
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Pesenti C, Beltrame L, Velle A, Fruscio R, Jaconi M, Borella F, Cribiù FM, Calura E, Venturini LV, Lenoci D, Agostinis F, Katsaros D, Panini N, Bianchi T, Landoni F, Miozzo M, D'Incalci M, Brenton JD, Romualdi C, Marchini S. Copy number alterations in stage I epithelial ovarian cancer highlight three genomic patterns associated with prognosis. Eur J Cancer 2022; 171:85-95. [PMID: 35714451 DOI: 10.1016/j.ejca.2022.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/13/2022] [Accepted: 05/03/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Stage I epithelial ovarian cancer (EOC) encompasses five histologically different subtypes of tumors confined to the ovaries with a generally favorable prognosis. Despite the intrinsic heterogeneity, all stage I EOCs are treated with complete resection and adjuvant therapy in most of the cases. Owing to the lack of robust prognostic markers, this often leads to overtreatment. Therefore, a better molecular characterization of stage I EOCs could improve the assessment of the risk of relapse and the refinement of optimal treatment options. MATERIALS AND METHODS 205 stage I EOCs tumor biopsies with a median follow-up of eight years were gathered from two independent Italian tumor tissue collections, and the genome distribution of somatic copy number alterations (SCNAs) was investigated by shallow whole genome sequencing (sWGS) approach. RESULTS Despite the variability in SCNAs distribution both across and within the histotypes, we were able to define three common genomic instability patterns, namely stable, unstable, and highly unstable. These patterns were based on the percentage of the genome affected by SCNAs and on their length. The genomic instability pattern was strongly predictive of patients' prognosis also with multivariate models including currently used clinico-pathological variables. CONCLUSIONS The results obtained in this study support the idea that novel molecular markers, in this case genomic instability patterns, can anticipate the behavior of stage I EOC regardless of tumor subtype and provide valuable prognostic information. Thus, it might be propitious to extend the study of these genomic instability patterns to improve rational management of this disease.
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Affiliation(s)
- Chiara Pesenti
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | | | - Angelo Velle
- Department of Biology, University of Padova, Padova, Italy
| | - Robert Fruscio
- Department of Obstetrics and Gynaecology, Università Degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Marta Jaconi
- Department of Pathology, Università Degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Fulvio Borella
- Gynecology and Obstetrics 1, Department of Surgical Sciences, San Anna Hospital, University of Torino, Torino, Italy
| | - Fulvia Milena Cribiù
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Enrica Calura
- Department of Biology, University of Padova, Padova, Italy
| | - Lara Veronica Venturini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Deborah Lenoci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | | | - Dionyssios Katsaros
- AOU City of Health, Dept of Surgical Sciences, Gynecology, St Anna Hospital and University of Torino, Torino, Italy
| | - Nicolò Panini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Tommaso Bianchi
- Department of Obstetrics and Gynaecology, Università Degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Fabio Landoni
- Department of Obstetrics and Gynaecology, Università Degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Monica Miozzo
- Department of Health Sciences, Medical Genetics, Università Degli Studi di Milano, Milano, Italy; Research Laboratories Coordination Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Maurizio D'Incalci
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, Rozzano, Italy; Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy.
| | - James D Brenton
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
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Hoffmann OI, Regenauer M, Czogalla B, Brambs C, Burges A, Mayer B. Interpatient Heterogeneity in Drug Response and Protein Biomarker Expression of Recurrent Ovarian Cancer. Cancers (Basel) 2022; 14:cancers14092279. [PMID: 35565408 PMCID: PMC9103312 DOI: 10.3390/cancers14092279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/24/2022] [Accepted: 04/29/2022] [Indexed: 12/10/2022] Open
Abstract
Recurrent ovarian-cancer patients face low 5-year survival rates despite chemotherapy. A variety of guideline-recommended second-line therapies are available, but they frequently result in trial-and-error treatment. Alterations and adjustments are common in the treatment of recurrent ovarian cancer. The drug response of 30 lesions obtained from 22 relapsed ovarian cancer patients to different chemotherapeutic and molecular agents was analyzed with the patient-derived ovarian-cancer spheroid model. The profile of druggable biomarkers was immunohistochemically assessed. The second-line combination therapy of carboplatin with gemcitabine was significantly superior to the combination of carboplatin with PEGylated liposomal doxorubicin (p < 0.0001) or paclitaxel (p = 0.0007). Except for treosulfan, all nonplatinum treatments tested showed a lesser effect on tumor spheroids compared to that of platinum-based therapies. Treosulfan showed the highest efficacy of all nonplatinum agents, with significant advantage over vinorelbine (p < 0.0001) and topotecan (p < 0.0001), the next best agents. The comparative testing of a variety of treatment options in the ovarian-cancer spheroid model resulted in the identification of more effective regimens for 30% of patients compared to guideline-recommended therapies. Recurrent cancers obtained from different patients revealed profound interpatient heterogeneity in the expression pattern of druggable protein biomarkers. In contrast, different lesions obtained from the same patient revealed a similar drug response and biomarker expression profile. Biological heterogeneity observed in recurrent ovarian cancers might explain the strong differences in the clinical drug response of these patients. Preclinical drug testing and biomarker profiling in the ovarian-cancer spheroid model might help in optimizing treatment management for individual patients.
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Affiliation(s)
| | - Manuel Regenauer
- Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 Munich, Germany;
| | - Bastian Czogalla
- Department of Obstetrics and Gynecology, Klinikum der Universität München, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 Munich, Germany; (B.C.); (A.B.)
| | - Christine Brambs
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University Munich, Ismaninger Straße 22, 81675 Munich, Germany;
| | - Alexander Burges
- Department of Obstetrics and Gynecology, Klinikum der Universität München, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 Munich, Germany; (B.C.); (A.B.)
| | - Barbara Mayer
- SpheroTec GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany;
- Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 Munich, Germany;
- German Cancer Consortium (DKTK), Partner Site Munich, Pettenkoferstraße 8a, 80336 Munich, Germany
- Correspondence: ; Tel.: +49-89-4400-76438
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Paracchini L, D’Incalci M, Marchini S. Liquid Biopsy in the Clinical Management of High-Grade Serous Epithelial Ovarian Cancer-Current Use and Future Opportunities. Cancers (Basel) 2021; 13:2386. [PMID: 34069200 PMCID: PMC8156052 DOI: 10.3390/cancers13102386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
The lack of a sensitive and specific biomarker and the limits relating to the single primary tumor sampling make it difficult to monitor high-grade serous epithelial ovarian cancer (HGS-EOC) over time and to capture those alterations that are potentially useful in guiding clinical decisions. To overcome these issues, liquid biopsy has emerged as a very promising tool for HGS-EOC. The analysis of circulating tumor DNA appears to be feasible and studies assessing specific pathogenic mutations (i.e., TP53) or copy number alterations have shown a sufficient degree of sensitivity and specificity to be realistically used to monitor the effectiveness of antitumor therapy. Liquid biopsy can also provide potential important information on the mechanisms of sensitivity and resistance, e.g., by the determination of the reversion of BRCA mutations. Perspective studies are needed to test whether the application of liquid biopsy will significantly improve HGS-EOC management and patients' survival.
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Affiliation(s)
- Lara Paracchini
- Department of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy;
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy;
| | - Maurizio D’Incalci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
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6
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Paracchini L, Beltrame L, Grassi T, Inglesi A, Fruscio R, Landoni F, Ippolito D, Delle Marchette M, Paderno M, Adorni M, Jaconi M, Romualdi C, D'Incalci M, Siravegna G, Marchini S. Genome-wide Copy-number Alterations in Circulating Tumor DNA as a Novel Biomarker for Patients with High-grade Serous Ovarian Cancer. Clin Cancer Res 2021; 27:2549-2559. [PMID: 33323403 DOI: 10.1158/1078-0432.ccr-20-3345] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 02/05/2023]
Abstract
PURPOSE High-grade serous epithelial ovarian cancer (HGS-EOC) is defined by high levels of somatic copy-number alterations (SCNA) with marked spatial and temporal tumor heterogeneity. Biomarkers serving to monitor drug response and detect disease recurrence are lacking, a fact which reflects an unmet clinical need. EXPERIMENTAL DESIGN A total of 185 plasma samples and 109 matched tumor biopsies were collected from 46 patients with HGS-EOC, and analyzed by shallow whole-genome sequencing (sWGS). The percentage of tumor fraction (TF) in the plasma was used to study the biological features of the disease at the time of diagnosis (T0) and correlated with patients' survival. Longitudinal analysis of TF was correlated with CA-125 levels and radiological images to monitor disease recurrence. RESULTS Gain in the clonal regions, 3q26.2 and 8q24.3, was observed in the 87.8% and 78.05% of plasma samples, suggesting that plasma sWGS mirrors solid biopsies. At T0, multivariate analysis revealed that plasma TF levels were an independent prognostic marker of relapse (P < 0.022). After platinum (Pt)-based treatment, circulating tumor DNA (ctDNA) analysis showed a change in the heterogeneous pattern of genomic amplification, including an increased frequency of amplification, compared with before Pt-based treatment in the 19p31.11 and 19q13.42 regions. TF in serially collected ctDNA samples outperformed CA-125 in anticipating clinical and radiological progression by 240 days (range, 37-491). CONCLUSIONS Our results support the notion that sWGS is an inexpensive and useful tool for the genomic analysis of ctDNA in patients with HGS-EOC to monitor disease evolution and to anticipate relapse better than serum CA-125, the routinely used clinical biomarker.See related commentary by Dhani, p. 2372.
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Affiliation(s)
- Lara Paracchini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Luca Beltrame
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Tommaso Grassi
- Department of Obstetrics and Gynaecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Alessia Inglesi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Robert Fruscio
- Department of Obstetrics and Gynaecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Fabio Landoni
- Department of Obstetrics and Gynaecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Davide Ippolito
- Department of Obstetrics and Gynaecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Martina Delle Marchette
- Department of Obstetrics and Gynaecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Mariachiara Paderno
- Department of Obstetrics and Gynaecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Marco Adorni
- Department of Obstetrics and Gynaecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Marta Jaconi
- Department of Pathology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | | | - Maurizio D'Incalci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy.
| | - Giulia Siravegna
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sergio Marchini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
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7
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Iqbal W, Demidova EV, Serrao S, ValizadehAslani T, Rosen G, Arora S. RRM2B Is Frequently Amplified Across Multiple Tumor Types: Implications for DNA Repair, Cellular Survival, and Cancer Therapy. Front Genet 2021; 12:628758. [PMID: 33868369 PMCID: PMC8045241 DOI: 10.3389/fgene.2021.628758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/23/2021] [Indexed: 01/21/2023] Open
Abstract
RRM2B plays a crucial role in DNA replication, repair and oxidative stress. While germline RRM2B mutations have been implicated in mitochondrial disorders, its relevance to cancer has not been established. Here, using TCGA studies, we investigated RRM2B alterations in cancer. We found that RRM2B is highly amplified in multiple tumor types, particularly in MYC-amplified tumors, and is associated with increased RRM2B mRNA expression. We also observed that the chromosomal region 8q22.3–8q24, is amplified in multiple tumors, and includes RRM2B, MYC along with several other cancer-associated genes. An analysis of genes within this 8q-amplicon showed that cancers that have both RRM2B-amplified along with MYC have a distinct pattern of amplification compared to cancers that are unaltered or those that have amplifications in RRM2B or MYC only. Investigation of curated biological interactions revealed that gene products of the amplified 8q22.3–8q24 region have important roles in DNA repair, DNA damage response, oxygen sensing, and apoptosis pathways and interact functionally. Notably, RRM2B-amplified cancers are characterized by mutation signatures of defective DNA repair and oxidative stress, and at least RRM2B-amplified breast cancers are associated with poor clinical outcome. These data suggest alterations in RR2MB and possibly the interacting 8q-proteins could have a profound effect on regulatory pathways such as DNA repair and cellular survival, highlighting therapeutic opportunities in these cancers.
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Affiliation(s)
- Waleed Iqbal
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,School of Biomedical Engineering, Science and Health Systems, Drexel University College of Engineering, Philadelphia, PA, United States
| | - Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Samantha Serrao
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Department of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University, Philadelphia, PA, United States
| | - Taha ValizadehAslani
- Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, United States
| | - Gail Rosen
- Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, United States
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States
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8
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High mRNA expression of LY6 gene family is associated with overall survival outcome in pancreatic ductal adenocarcinoma. Oncotarget 2021; 12:145-159. [PMID: 33613843 PMCID: PMC7869573 DOI: 10.18632/oncotarget.27880] [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: 11/21/2020] [Accepted: 01/19/2021] [Indexed: 11/30/2022] Open
Abstract
Pancreatic cancer ranks one of the worst in overall survival outcome with a 5 year survival rate being less than 10%. Pancreatic cancer faces unique challenges in its diagnosis and treatment, such as the lack of clinically validated biomarkers and the immensely immunosuppressive tumor microenvironment. Recently, the LY6 gene family has received increasing attention for its multi-faceted roles in cancer development, stem cell maintenance, immunomodulation, and association with more aggressive and hard-to-treat cancers. A detailed study of mRNA expression of LY6 gene family and its association with overall survival (OS) outcome in pancreatic cancers is lacking. We used publicly available clinical datasets to analyze the mRNA expression of a set of LY6 genes and its effect on OS outcome in the context of the tumor microenvironment and immunomodulation. We used web-based tools Kaplan-Meier Plotter, cBioPortal, Oncomine and R-programming to analyze copy number alterations, mRNA expression and its association with OS outcome in pancreatic cancer. These analyses demonstrated that high expression of LY6 genes is associated with OS and disease free survival (DFS) outcome. High expression of LY6 genes and their association with OS outcome is dependent on the composition of tumor microenvironment. Considering that LY6 proteins are anchored to the outer cell membrane or secreted, making them readily accessible, these findings highlight the potential of LY6 family members in the future of pancreatic cancer diagnosis and treatment.
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9
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Dorsett KA, Jones RB, Ankenbauer KE, Hjelmeland AB, Bellis SL. Sox2 promotes expression of the ST6Gal-I glycosyltransferase in ovarian cancer cells. J Ovarian Res 2019; 12:93. [PMID: 31610800 PMCID: PMC6792265 DOI: 10.1186/s13048-019-0574-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/25/2019] [Indexed: 12/15/2022] Open
Abstract
Background The ST6Gal-I glycosyltransferase, which adds α2–6-linked sialic acids to N-glycosylated proteins is upregulated in a wide range of malignancies including ovarian cancer. Prior studies have shown that ST6Gal-I-mediated sialylation of select surface receptors remodels intracellular signaling to impart cancer stem cell (CSC) characteristics. However, the mechanisms that contribute to ST6Gal-I expression in stem-like cancer cells are poorly understood. Results Herein, we identify the master stem cell transcription factor, Sox2, as a novel regulator of ST6Gal-I expression. Interestingly, SOX2 and ST6GAL1 are located within the same tumor-associated amplicon, 3q26, and these two genes exhibit coordinate gains in copy number across multiple cancers including ~ 25% of ovarian serious adenocarcinomas. In conjunction with genetic co-amplification, our studies suggest that Sox2 directly binds the ST6GAL1 promoter to drive transcription. ST6Gal-I expression is directed by at least four distinct promoters, and we identified the P3 promoter as the predominant promoter utilized by ovarian cancer cells. Chromatin Immunoprecipitation (ChIP) assays revealed that Sox2 binds regions proximal to the P3 promoter. To confirm that Sox2 regulates ST6Gal-I expression, Sox2 was either overexpressed or knocked-down in various ovarian cancer cell lines. Sox2 overexpression induced an increase in ST6Gal-I mRNA and protein, as well as surface α2–6 sialylation, whereas Sox2 knock-down suppressed levels of ST6Gal-I mRNA, protein and surface α2–6 sialylation. Conclusions These data suggest a process whereby SOX2 and ST6GAL1 are coordinately amplified in cancer cells, with the Sox2 protein then binding the ST6GAL1 promoter to further augment ST6Gal-I expression. Our collective results provide new insight into mechanisms that upregulate ST6Gal-I expression in ovarian cancer cells, and also point to the possibility that some of the CSC characteristics commonly attributed to Sox2 may, in part, be mediated through the sialyltransferase activity of ST6Gal-I.
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Affiliation(s)
- Kaitlyn A Dorsett
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, MCLM 350, 1918 University Boulevard, Birmingham, AL, 35294, USA
| | - Robert B Jones
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, MCLM 350, 1918 University Boulevard, Birmingham, AL, 35294, USA
| | - Katherine E Ankenbauer
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, MCLM 350, 1918 University Boulevard, Birmingham, AL, 35294, USA
| | - Anita B Hjelmeland
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, MCLM 350, 1918 University Boulevard, Birmingham, AL, 35294, USA
| | - Susan L Bellis
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, MCLM 350, 1918 University Boulevard, Birmingham, AL, 35294, USA.
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Dugo M, Devecchi A, De Cecco L, Cecchin E, Mezzanzanica D, Sensi M, Bagnoli M. Focal Recurrent Copy Number Alterations Characterize Disease Relapse in High Grade Serous Ovarian Cancer Patients with Good Clinical Prognosis: A Pilot Study. Genes (Basel) 2019; 10:genes10090678. [PMID: 31491988 PMCID: PMC6770978 DOI: 10.3390/genes10090678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 02/01/2023] Open
Abstract
High grade serous ovarian cancer (HGSOC) retains high molecular heterogeneity and genomic instability, which currently limit the treatment opportunities. HGSOC patients receiving complete cytoreduction (R0) at primary surgery and platinum-based therapy may unevenly experience early disease relapse, in spite of their clinically favorable prognosis. To identify distinctive traits of the genomic landscape guiding tumor progression, we focused on the R0 patients of The Cancer Genome Atlas (TCGA) ovarian serous cystadenocarcinoma (TCGA-OV) dataset and classified them according to their time to relapse (TTR) from surgery. We included in the study two groups of R0-TCGA patients experiencing substantially different outcome: Resistant (R; TTR ≤ 12 months; n = 11) and frankly Sensitive (fS; TTR ≥ 24 months; n = 16). We performed an integrated clinical, RNA-Sequencing, exome and somatic copy number alteration (sCNA) data analysis. No significant differences in mutational landscape were detected, although the lack of BRCA-related mutational signature characterized the R group. Focal sCNA analysis showed a higher frequency of amplification in R group and deletions in fS group respectively, involving cytobands not commonly detected by recurrent sCNA analysis. Functional analysis of focal sCNA with a concordantly altered gene expression identified in R group a gain in Notch, and interferon signaling and fatty acid metabolism. We are aware of the constraints related to the low number of OC cases analyzed. It is worth noting, however, that the sCNA identified in this exploratory analysis and characterizing Pt-resistance are novel, deserving validation in a wider cohort of patients achieving complete surgical debulking.
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Affiliation(s)
- Matteo Dugo
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Andrea Devecchi
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Loris De Cecco
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico, IRCCS National Cancer Institute, 33081 Aviano, Pordenone, Italy.
| | - Delia Mezzanzanica
- Molecular Therapy Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Marialuisa Sensi
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Marina Bagnoli
- Molecular Therapy Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
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