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Hassan AN, Mustafa MS. Breast Cancer High-Penetrance Genes BRCA1 and BRCA2 Mutations Using Next-Generation Sequencing Among Iraqi Kurdish Women. Cureus 2024; 16:e62160. [PMID: 38863777 PMCID: PMC11166091 DOI: 10.7759/cureus.62160] [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] [Accepted: 06/10/2024] [Indexed: 06/13/2024] Open
Abstract
Background BRCA1 and BRCA2 genes are the main high-penetrance genes that are responsible for most cases of inherited breast cancer. The present study aimed to detect the frequencies of inherited breast cancer caused by BRCA1 and BRCA2 genes among Kurdish breast cancer patients, including all the exome of these two genes, using next-generation sequencing (NGS). Methodology Seventy women who were diagnosed with breast cancer and registered at Nanakali Hospital in Erbil, Iraq, were included. Blood samples were collected for molecular testing (polymerase chain reaction (PCR)) targeting all exomes of BRCA1 and BRCA2 genes. All exome regions are sequenced by NGS using the Miseq system (Illumina Inc., San Diego, CA). Obtained data were visualized using Integrative Genomics Viewer (IGV 2.3 Software, Broad Institute, Cambridge, MA). Data were interpreted based on the National Center for Biotechnology Information (NCBI), Clinically Relevant Variation (ClinVar) archives, and other databases. Results Among 70 samples, more than forty-two variants have been detected, 20 on BRCA1 and 22 on BRCA2. Regarding clinical significance, six (14.28%) variants were pathogenic, four of them on the BRCA1 gene, which were: c.3607C>T, c.3544C>T, c.68_69del, and c.224_227delAAAG, and two pathogenic variants were on BRCA2 gene: c.100G>T, and c.1813delA. Also, two (4.76%) variants were conflict interpretations of pathogenicity, one (2.38%) was a variant of uncertain significant VUS, and the rest 29 (69%) variants were benign. In addition, four new variants (three in BRCA1 and one in BRCA2 gene), never previously reported, were identified. Conclusions In conclusion, analyzing the BRCA1/2 genes provide a better prediction for the risk of developing breast cancer in the future. Variant types and frequencies differ among different populations and ethnicities, the common mutations worldwide may not be prevalent in the Kurdish population. The current research findings will be useful for future screening studies of these two genes in the Kurdish population.
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Affiliation(s)
- Ahmad N Hassan
- Department of Medical Laboratory Technology, Erbil Technical Health and Medical College, Erbil Polytechnic University, Erbil, IRQ
| | - Mustafa S Mustafa
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, IRQ
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2
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Bianchi A, Zelli V, D’Angelo A, Di Matteo A, Scoccia G, Cannita K, Dimas A, Glentis S, Zazzeroni F, Alesse E, Di Marco A, Tessitore A. A method to comprehensively identify germline SNVs, INDELs and CNVs from whole exome sequencing data of BRCA1/2 negative breast cancer patients. NAR Genom Bioinform 2024; 6:lqae033. [PMID: 38633426 PMCID: PMC11023157 DOI: 10.1093/nargab/lqae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
In the rapidly evolving field of genomics, understanding the genetic basis of complex diseases like breast cancer, particularly its familial/hereditary forms, is crucial. Current methods often examine genomic variants-such as Single Nucleotide Variants (SNVs), insertions/deletions (Indels), and Copy Number Variations (CNVs)-separately, lacking an integrated approach. Here, we introduced a robust, flexible methodology for a comprehensive variants' analysis using Whole Exome Sequencing (WES) data. Our approach uniquely combines meticulous validation with an effective variant filtering strategy. By reanalyzing two germline WES datasets from BRCA1/2 negative breast cancer patients, we demonstrated our tool's efficiency and adaptability, uncovering both known and novel variants. This contributed new insights for potential diagnostic, preventive, and therapeutic strategies. Our method stands out for its comprehensive inclusion of key genomic variants in a unified analysis, and its practical resolution of technical challenges, offering a pioneering solution in genomic research. This tool presents a breakthrough in providing detailed insights into the genetic alterations in genomes, with significant implications for understanding and managing hereditary breast cancer.
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Affiliation(s)
- Andrea Bianchi
- Department of Information Engineering, Computer Science and Mathematics, University of L’Aquila, L’Aquila 67100, Italy
| | - Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila 67100, Italy
| | - Andrea D’Angelo
- Department of Information Engineering, Computer Science and Mathematics, University of L’Aquila, L’Aquila 67100, Italy
| | - Alessandro Di Matteo
- Department of Information Engineering, Computer Science and Mathematics, University of L’Aquila, L’Aquila 67100, Italy
| | - Giulia Scoccia
- Department of Information Engineering, Computer Science and Mathematics, University of L’Aquila, L’Aquila 67100, Italy
| | - Katia Cannita
- Oncology Division, Mazzini Hospital, ASL Teramo, Teramo 64100, Italy
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center, Alexander Fleming, Vari 16672, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center, Alexander Fleming, Vari 16672, Greece
- Pediatric Hematology/Oncology Unit (POHemU), First Department of Pediatrics, University of Athens, Aghia Sophia Children’s Hospital, Athens 11527, Grece
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila 67100, Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila 67100, Italy
| | - Antinisca Di Marco
- Department of Information Engineering, Computer Science and Mathematics, University of L’Aquila, L’Aquila 67100, Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila 67100, Italy
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Richau CS, Scherer NDM, Matta BP, de Armas EM, de Barros Moreira FC, Bergmann A, Pereira Chaves CB, Boroni M, dos Santos ACE, Moreira MAM. BRCA1, BRCA2, and TP53 germline and somatic variants and clinicopathological characteristics of Brazilian patients with epithelial ovarian cancer. Cancer Med 2024; 13:e6729. [PMID: 38308422 PMCID: PMC10905552 DOI: 10.1002/cam4.6729] [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: 06/21/2023] [Revised: 10/20/2023] [Accepted: 11/07/2023] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Approximately 3/4 of ovarian cancers are diagnosed in advanced stages, with the high-grade epithelial ovarian carcinoma (EOC) accounting for 90% of the cases. EOC present high genomic instability and somatic loss-of-function variants in genes associated with homologous recombination mutational repair pathway (HR), such as BRCA1 and BRCA2, and in TP53. The identification of germline variants in HR genes in EOC is relevant for treatment of platinum resistant tumors and relapsed tumors with therapies based in synthetic lethality such as PARP inhibitors. Patients with somatic variants in HR genes may also benefit from these therapies. In this work was analyzed the frequency of somatic variants in BRCA1, BRCA2, and TP53 in an EOC cohort of Brazilian patients, estimating the proportion of variants in tumoral tissue and their association with progression-free survival and overall survival. METHODS The study was conducted with paired blood/tumor samples from 56 patients. Germline and tumoral sequences of BRCA1, BRCA2, and TP53 were obtained by massive parallel sequencing. The HaplotypeCaller method was used for calling germline variants, and somatic variants were called with Mutect2. RESULTS A total of 26 germline variants were found, and seven patients presented germline pathogenic or likely pathogenic variants in BRCA1 or BRCA2. The analysis of tumoral tissue identified 52 somatic variants in 41 patients, being 43 somatic variants affecting or likely affecting protein functionality. Survival analyses showed that tumor staging was associated with overall survival (OS), while the presence of somatic mutation in TP53 was not associated with OS or progression-free survival. CONCLUSION Frequency of pathogenic or likely pathogenic germline variants in BRCA1 and BRCA2 (12.5%) was lower in comparison with other studies. TP53 was the most altered gene in tumors, with 62.5% presenting likely non-functional or non-functional somatic variants, while eight 14.2% presented likely non-functional or non-functional somatic variants in BRCA1 or BRCA2.
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Affiliation(s)
| | | | - Bruna Palma Matta
- Tumoral Genetics and Virology ProgramInstituto Nacional de CâncerRio de JaneiroBrazil
- Present address:
Hospital BP ‐ A Beneficência Portuguesa de São PauloSão PauloBrazil
| | | | | | - Anke Bergmann
- Clinical EpidemiologyInstituto Nacional de CâncerRio de JaneiroBrazil
| | | | - Mariana Boroni
- Bioinformatics and Computational Biology LaboratoryInstituto Nacional de CâncerRio de JaneiroBrazil
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Wei X, Tian Z, Zhao F, Sun A, Zhao S, Jamil M, Yan W. Unveiling pathogenic mutations in BRCA1 and BRCA2 genes across head and neck squamous cell carcinoma patients via next generation sequencing. Am J Cancer Res 2023; 13:6099-6112. [PMID: 38187047 PMCID: PMC10767334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSC) presents a formidable challenge in the field of oncology due to its aggressive nature and the limited therapeutic options available. In this study, our primary focus was on the Pakistani HNSC patient population, aiming to investigate germline oncogenic mutations within the BRCA1 and BRCA2 genes via Next Generation Sequencing (NGS) and explore their clinical implications. We sought to understand the functional consequences of these mutations via RT-qPCR and Immunohistochemistry (IHC) techniques. The key discovery of our research lies in the identification of three pathogenic mutations, including two within BRCA1 (p.Cys274Ter and p.Glu272Ter) and one within BRCA2 (p.Met1Val), among Pakistani HNSC patients. These mutations previously associated with an increased risk of various cancers. What sets our study apart is the uniqueness of these pathogenic mutations, absent in HNSC patients from other populations. This suggests a distinct genetic profile in Pakistani HNSC patients, possibly contributing to their susceptibility to this malignancy. Furthermore, our research revealed elevated expression levels of BRCA1 and BRCA2 genes in HNSC samples harboring pathogenic mutations, offering insights into mechanisms driving tumor progression in HNSC. Importantly, we identified significant enrichment of BRCA1/2 genes in pathways related to cancer development within the KEGG database. Finally, in our quest to explore therapeutic avenues, we systematically analyzed drugs targeting up-regulated and mutated BRCA1/2 genes, identifying promising candidates for tailored treatment modalities in HNSC. In conclusion, our study reveals the unique genetic profile of HNSC in Pakistani patients, featuring unique pathogenic mutations in BRCA1 and BRCA2 genes. These mutations offer promise as valuable diagnostic markers and potential therapeutic targets.
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Affiliation(s)
- Xiaotong Wei
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Zhizhengrong Tian
- Department of Ultrasound, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Fengyun Zhao
- Department of Ultrasound, Cangzhou Maternal and Child Health Care HospitalCangzhou 061000, Hebei, China
| | - Anjun Sun
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Shujuan Zhao
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Wei Yan
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
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5
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Golan T, Casolino R, Biankin AV, Hammel P, Whitaker KD, Hall MJ, Riegert-Johnson DL. Germline BRCA testing in pancreatic cancer: improving awareness, timing, turnaround, and uptake. Ther Adv Med Oncol 2023; 15:17588359231189127. [PMID: 37720496 PMCID: PMC10504836 DOI: 10.1177/17588359231189127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/04/2023] [Indexed: 09/19/2023] Open
Abstract
Prognosis is generally poor for patients with pancreatic ductal adenocarcinoma. However, patients with germline BRCA1 or BRCA2 mutations (gBRCAm) may benefit from first-line platinum-based chemotherapy and maintenance therapy with the poly(adenosine diphosphate-ribose) polymerase inhibitor olaparib following at least 16 weeks of first-line platinum-based chemotherapy without disease progression. Germline breast cancer gene (BRCA) testing is therefore important to ensure that patients receive the most effective treatment. In addition, testing for other DNA damage response gene mutations beyond gBRCAm may also guide treatment decisions. However, clinical pathways for genetic testing are often suboptimal, leading to delays in treatment initiation or missed opportunities for personalized therapy. Barriers to testing include low rates of referral and uptake, delays to referral and slow result turnaround times, cost, and biopsy and assay limitations if somatic testing is performed, leading to the requirement for subsequent dedicated germline testing. Low rates of referral may result from lack of awareness among physicians of the clinical value of testing, coupled with low confidence in interpreting test results and poor availability of genetic counseling services. Among patients, barriers to uptake may include similar lack of awareness of the clinical value of testing, anxiety regarding the implications of test results, lack of insurance coverage, fear of negative insurance implications, and socioeconomic factors. Potential solutions include innovative approaches to testing pathways, including 'mainstreaming' of testing in which BRCA tests are routinely arranged by the treating oncologist, with the involvement of genetic counselors if a patient is found to have a gBRCAm. More recently, the utility of multigene panel analyses has also been explored. Access to genetic counseling may also be improved through initiatives such as having a genetic counseling appointment for all new patient visits and telemedicine approaches, including the use of telephone consultations or DVD-assisted counseling. Educational programs will also be beneficial, and cost effectiveness is likely to improve as the number of targeted treatments increases and when the earlier detection of tumors in family members following cascade testing is considered.
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Affiliation(s)
- Talia Golan
- Institute of Oncology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia
| | - Pascal Hammel
- Department of Digestive and Medical Oncology, University Paris-Saclay, Paul Brousse Hospital (AP-HP), Villejuif, France
| | - Kristen D. Whitaker
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael J. Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
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Abdel-Razeq H. Surgical options for patients with early-stage breast cancer and pathogenic germline variants: an oncologist perspectives. Front Oncol 2023; 13:1265197. [PMID: 37781190 PMCID: PMC10539549 DOI: 10.3389/fonc.2023.1265197] [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: 07/22/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Breast cancer continues to be the most common cancer diagnosed among women worldwide. Family history of breast cancer is frequently encountered, and 5-15% of patients may carry inherited pathogenic germline variants, identification of which can be helpful for both; patients themselves and their unaffected close relatives. The availability and affordability of molecular diagnostics, like next generation sequencing (NGS), had resulted in wider adoption of such technologies to detect pathogenic variants of cancer-predisposing genes. International guidelines had recently broadened the indications for germline genetic testing to include much more patients, and also expanded the testing to include multi-gene panels, while some professional societies are calling for universal testing of all newly diagnosed patients with breast cancer, regardless of their age, personal or family history. The risk of experiencing a contralateral breast cancer (CBC) or ipsilateral recurrence, is well known. Such risk is highest with variants like BRCA1 and BRCA2, but less well-studied with other less common variants. The optimal local therapy for women with BRCA-associated breast cancer remains controversial, but tends to be aggressive and may involve bilateral mastectomies, which may not have any survival advantage. Additionally, surgical management of unaffected women, known to carry a pathogenic cancer-predisposing gene, may vary from surveillance to bilateral mastectomies, too. The oncological safety, and the higher satisfaction of unaffected women and patients with new surgical techniques, like the skin-sparing (SSM) and nipple-sparing (NSM) mastectomies, eased up the process of counselling. In this review, we address the oncological safety of less aggressive surgical options for both; patients and unaffected carriers.
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Affiliation(s)
- Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, Amman, Jordan
- School of Medicine, The University of Jordan, Amman, Jordan
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7
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Bucalo A, Conti G, Valentini V, Capalbo C, Bruselles A, Tartaglia M, Bonanni B, Calistri D, Coppa A, Cortesi L, Giannini G, Gismondi V, Manoukian S, Manzella L, Montagna M, Peterlongo P, Radice P, Russo A, Tibiletti MG, Turchetti D, Viel A, Zanna I, Palli D, Silvestri V, Ottini L. Male breast cancer risk associated with pathogenic variants in genes other than BRCA1/2: an Italian case-control study. Eur J Cancer 2023; 188:183-191. [PMID: 37262986 DOI: 10.1016/j.ejca.2023.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Germline pathogenic variants (PVs) in BRCA1/2 genes are associated with breast cancer (BC) risk in both women and men. Multigene panel testing is being increasingly used for BC risk assessment, allowing the identification of PVs in genes other than BRCA1/2. While data on actionable PVs in other cancer susceptibility genes are now available in female BC, reliable data are still lacking in male BC (MBC). This study aimed to provide the patterns, prevalence and risk estimates associated with PVs in non-BRCA1/2 genes for MBC in order to improve BC prevention for male patients. METHODS We performed a large case-control study in the Italian population, including 767 BRCA1/2-negative MBCs and 1349 male controls, all screened using a custom 50 cancer gene panel. RESULTS PVs in genes other than BRCA1/2 were significantly more frequent in MBCs compared with controls (4.8% vs 1.8%, respectively) and associated with a threefold increased MBC risk (OR: 3.48, 95% CI: 1.88-6.44; p < 0.0001). PV carriers were more likely to have personal (p = 0.03) and family (p = 0.02) history of cancers, not limited to BC. PALB2 PVs were associated with a sevenfold increased MBC risk (OR: 7.28, 95% CI: 1.17-45.52; p = 0.034), and ATM PVs with a fivefold increased MBC risk (OR: 4.79, 95% CI: 1.12-20.56; p = 0.035). CONCLUSIONS This study highlights the role of PALB2 and ATM PVs in MBC susceptibility and provides risk estimates at population level. These data may help in the implementation of multigene panel testing in MBC patients and inform gender-specific BC risk management and decision making for patients and their families.
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Affiliation(s)
- Agostino Bucalo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giulia Conti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Daniele Calistri
- Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori"-IRST IRCCS, Meldola, Italy
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, University of Modena and Reggio Emilia, Modena, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Viviana Gismondi
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Siranoush Manoukian
- Unità di Genetica Medica, Dipartimento di Oncologia Medica ed Ematologia, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Livia Manzella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori (INT), Milan, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Maria Grazia Tibiletti
- Dipartimento di Patologia, ASST Settelaghi and Centro di Ricerca per lo studio dei tumori eredo-familiari, Università dell'Insubria, Varese, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Alessandra Viel
- Unità di Oncogenetica e Oncogenomica Funzionale, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Ines Zanna
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | - Domenico Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Florence, Italy
| | | | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.
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Tong A, Di X, Zhao X, Liang X. Review the progression of ovarian clear cell carcinoma from the perspective of genomics and epigenomics. Front Genet 2023; 14:952379. [PMID: 36873929 PMCID: PMC9978161 DOI: 10.3389/fgene.2023.952379] [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: 05/25/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a rare subtype of epithelial ovarian cancer with unique molecular characteristics, specific biological and clinical behavior, poor prognosis and high resistance to chemotherapy. Pushed by the development of genome-wide technologies, our knowledge about the molecular features of OCCC has been considerably advanced. Numerous studies are emerging as groundbreaking, and many of them are promising treatment strategies. In this article, we reviewed studies about the genomics and epigenetics of OCCC, including gene mutation, copy number variations, DNA methylation and histone modifications.
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Affiliation(s)
- An Tong
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiangjie Di
- Clinical Trial Center, NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drugs, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiao Liang
- Department of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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9
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Wang M, Fu X, Wang W, Zhang Y, Jiang Z, Gu Y, Chu M, Shao Y, Li S. Comprehensive bioinformatics analysis confirms RBMS3 as the central candidate biological target for ovarian cancer. Med Eng Phys 2022; 110:103883. [PMID: 36075788 DOI: 10.1016/j.medengphy.2022.103883] [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: 06/25/2022] [Revised: 07/31/2022] [Accepted: 08/31/2022] [Indexed: 01/18/2023]
Abstract
Ovarian cancer (OC) is one of the most lethal malignancies in the female reproductive system. To find genes related to cancer progression targeting specific biological factors for targeted therapy, bioinformatics technology has been widely used. To screen the prognostic gene markers of OC by bioinformatics and explore their potential molecular biological mechanisms. Two data sets related to OC, GSE54388, and GSE119056, were rooted in the open comprehensive gene expression database (GEO). To correct the background of the data, standardize and screen differentially expressed genes (DEGs) using the R software limma package. The selected DEGs were enriched by Gene Ontology (GO) and through DAVID online database. Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathway analysis and protein-protein interaction network (PPI-network) map were constructed by STRING online database and Cytoscape software. Combined with the TCGA database, univariate and multivariate COX regression were used to screen prognostic genes. QRT-PCR was used to verify DEGs in clinical tissue samples. Eventually, the function of RBMS3 on the viability, migration, invasion, and apoptosis of OC cells was tested through functional experiments in vitro. 352 common DEGs were screened from GSE54388 and GSE119056 data sets. Survival analysis showed that MEIS2, TSTA3, CNTN1, RBMS3, and TRA2A were considered to be connected with the prognosis of OC. We discover that the expression level of RBMS3 was positively connected with the overall survival (OS) rate of sufferers with OC. The level of RBMS3 in OC tissues was markedly lower than that in neighboring structures and the outcomes of the GEPIA database were consistent with those of the qRT-PCR experiment. Through gene transfection technology it was found that overexpression of RBMS3 in OC cells substantially suppressed the vitality, migration, and invasion of OC cells and raised the rates of apoptosis in the OC cells. In this experiment, we distinguish 5 genes that may participate in the prognosis of OC and showed the key genes and pathways related to OC. It is speculated that RBMS3, a tumor suppressor gene, can be applied as a potential biological marker for the treatment of OC, gene expression summary, and prognosis.
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Affiliation(s)
- Mei Wang
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China.
| | - Xiangjun Fu
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China
| | - Wei Wang
- Wannan Medical College, Wuhu 241002, Anhui, China
| | - Yuan Zhang
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China
| | - Zhenyi Jiang
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China
| | - Yan Gu
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China
| | - Menglong Chu
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China
| | - Yanting Shao
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China
| | - Shuqin Li
- The First Affiliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu 241001, Anhui, China; Wannan Medical College, Wuhu 241002, Anhui, China.
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10
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Lund Johansen E, Fribert Thusgaard C, Thomassen M, Eriksen Boonen S, Marie Jochumsen K. Germline Pathogenic Variants Associated with Ovarian Cancer: A Historical Overview. Gynecol Oncol Rep 2022; 44:101105. [DOI: 10.1016/j.gore.2022.101105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
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11
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Herzog H, Dogan S, Aktas B, Nel I. Targeted Sequencing of Plasma-Derived vs. Urinary cfDNA from Patients with Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:4101. [PMID: 36077638 PMCID: PMC9454533 DOI: 10.3390/cancers14174101] [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: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
In breast cancer, the genetic profiling of circulating cell-free DNA (cfDNA) from blood plasma was shown to have good potential for clinical use. In contrast, only a few studies were performed investigating urinary cfDNA. In this pilot study, we analyzed plasma-derived and matching urinary cfDNA samples obtained from 15 presurgical triple-negative breast cancer patients. We used a targeted next-generation sequencing approach to identify and compare genetic alterations in both body fluids. The cfDNA concentration was higher in urine compared to plasma, but there was no significant correlation between matched samples. Bioinformatical analysis revealed a total of 3339 somatic breast-cancer-related variants (VAF ≥ 3%), whereof 1222 vs. 2117 variants were found in plasma-derived vs. urinary cfDNA, respectively. Further, 431 shared variants were found in both body fluids. Throughout the cohort, the recovery rate of plasma-derived mutations in matching urinary cfDNA was 47% and even 63% for pathogenic variants only. The most frequently occurring pathogenic and likely pathogenic mutated genes were NF1, CHEK2, KMT2C and PTEN in both body fluids. Notably, a pathogenic CHEK2 (T519M) variant was found in all 30 samples. Taken together, our results indicated that body fluids appear to be valuable sources bearing complementary information regarding the genetic tumor profile.
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Affiliation(s)
- Henrike Herzog
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Senol Dogan
- Soft Matter Physics Division, Peter-Debye-Institute, University of Leipzig, 04103 Leipzig, Germany
| | - Bahriye Aktas
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
| | - Ivonne Nel
- Department of Gynecology, Medical Center, University of Leipzig, 04103 Leipzig, Germany
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12
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BenAyed-Guerfali D, Kifagi C, BenKridis-Rejeb W, Ammous-Boukhris N, Ayedi W, Khanfir A, Daoud J, Mokdad-Gargouri R. The Identification by Exome Sequencing of Candidate Genes in BRCA-Negative Tunisian Patients at a High Risk of Hereditary Breast/Ovarian Cancer. Genes (Basel) 2022; 13:genes13081296. [PMID: 35893033 PMCID: PMC9331434 DOI: 10.3390/genes13081296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Germline variants in BRCA1/BRCA2 genes explain about 20% of hereditary breast/ovarian cancer (HBOC) cases. In the present paper, we aim to identify genetic determinants in BRCA-negative families from the South of Tunisia. (2) Methods: Exome Sequencing (ES) was performed on the lymphocyte DNA of patients negative for BRCA mutations from each Tunisian family with a high risk of HBOC. (3) Results: We focus on the canonical genes associated with HBOC and identified missense variants in DNA damage response genes, such as ATM, RAD52, and RAD54; however, no variants in PALB2, Chek2, and TP53 genes were found. To identify novel candidate genes, we selected variants harboring a loss of function and identified 17 stop-gain and 11 frameshift variants in genes not commonly known to be predisposed to HBOC. Then, we focus on rare and high-impact genes shared by at least 3 unrelated patients from each family and selected 16 gene variants. Through combined data analysis from MCODE with gene ontology and KEGG pathways, a short list of eight candidate genes (ATM, EP300, LAMA1, LAMC2, TNNI3, MYLK, COL11A2, and LAMB3) was created. The impact of the 24 selected genes on survival was analyzed using the TCGA data resulting in a selection of five candidate genes (EP300, KMT2C, RHPN2, HSPG2, and CCR3) that showed a significant association with survival. (4) Conclusions: We identify novel candidate genes predisposed to HBOC that need to be validated in larger cohorts and investigated by analyzing the co-segregation of selected variants in affected families and the locus-specific loss of heterozygosity to highlight their relevance for HBOC risk.
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Affiliation(s)
- Dorra BenAyed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Chamseddine Kifagi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Wala BenKridis-Rejeb
- Department of Medical Oncology, Habib Bourguiba Hospital, Sfax 3002, Tunisia; (W.B.-R.); (A.K.)
| | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Wajdi Ayedi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Afef Khanfir
- Department of Medical Oncology, Habib Bourguiba Hospital, Sfax 3002, Tunisia; (W.B.-R.); (A.K.)
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, Sfax 3002, Tunisia;
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
- Correspondence: ; Tel./Fax: +216-748-744-49
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13
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Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Devilee P, Tavtigian S, Bader GD, Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J. Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry. Cancers (Basel) 2022; 14:cancers14143363. [PMID: 35884425 PMCID: PMC9317824 DOI: 10.3390/cancers14143363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 01/27/2023] Open
Abstract
Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes.
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Affiliation(s)
- Martine Dumont
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Charles Joly-Beauparlant
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Arnaud Droit
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Stéphane Dubois
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Annie-Claude Collin-Deschesnes
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Penny Soucy
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Maxime Vallée
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Frédéric Fournier
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Audrey Lemaçon
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Muriel A. Adank
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, 24105 Kiel, Germany;
| | - Margreet G. E. M. Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, 3584 Utrecht, The Netherlands;
| | - Riccardo Berutti
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shelley Bull
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Michael R. Dufault
- Precision Medicine and Computational Biology, Sanofi Genzyme, Cambridge, MA 02142, USA;
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany;
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University of Würzburg, 97074 Würzburg, Germany;
| | | | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Jessica Green
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany;
| | - Mohamed Helmy
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
| | - Julia Hentschel
- Institute of Human Genetics, University Leipzig, 04103 Leipzig, Germany;
| | - Frans B. L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Judit Horváth
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany;
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 Rotterdam, The Netherlands;
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Da Kuang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Wolfgang Maier
- German Center for Neurodegenerative Diseases (DZNE), Department of Neurodegenerative Diseases and Geriatric Psychiatry, Medical Faculty, University Hospital Bonn, 53127 Bonn, Germany;
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany;
| | - Claus-Eric Ott
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 13353 Berlin, Germany;
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Department of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Alfredo Ramirez
- Division for Neurogenetics and Molecular Psychiatry, Medical Faculty, University of Cologne, 50937 Cologne, Germany;
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany;
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Antje Stäbler
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany;
| | - Tim M. Strom
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Christi J. van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
| | - Lizet van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Rob B. van der Luijt
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
- Department of Medical Genetics, University Medical Center, 3584 Utrecht, The Netherlands
| | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany;
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 Amsterdam, The Netherlands;
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University of Ulm, 89081 Ulm, Germany;
| | - Bernhard H. F. Weber
- Institute of Human Genetics, Regensburg University, 93053 Regensburg, Germany;
- Institute of Clinical Human Genetics, University Hospital Regensburg, 93053 Regensburg, Germany
| | | | | | - Peter Devilee
- Department of Pathology, Department of Human Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands;
| | - Sean Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Gary D. Bader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - David E. Goldgar
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Jacques Simard
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +418-654-2264
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Minigene Splicing Assays Identify 20 Spliceogenic Variants of the Breast/Ovarian Cancer Susceptibility Gene RAD51C. Cancers (Basel) 2022; 14:cancers14122960. [PMID: 35740625 PMCID: PMC9221245 DOI: 10.3390/cancers14122960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
RAD51C loss-of-function variants are associated with an increased risk of breast and ovarian cancers. Likewise, splicing disruptions are a frequent mechanism of gene inactivation. Taking advantage of a previous splicing-reporter minigene with exons 2-8 (mgR51C_ex2-8), we proceeded to check its impact on the splicing of candidate ClinVar variants. A total of 141 RAD51C variants at the intron/exon boundaries were analyzed with MaxEntScan. Twenty variants were selected and genetically engineered into the wild-type minigene. All the variants disrupted splicing, and 18 induced major splicing anomalies without any trace or minimal amounts (<2.4%) of the minigene full-length (FL) transcript. Twenty-seven transcripts (including the wild-type and r.904A FL transcripts) were identified by fluorescent fragment electrophoresis; of these, 14 were predicted to truncate the RAD51C protein, 3 kept the reading frame, and 8 minor isoforms (1.1−4.7% of the overall expression) could not be characterized. Finally, we performed a tentative interpretation of the variants according to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, classifying 16 variants as likely pathogenic. Minigene assays have been proven as valuable tools for the initial characterization of potential spliceogenic variants. Hence, minigene mgR51C_ex2-8 provided useful splicing data for 40 RAD51C variants.
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15
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Feasibility of targeted cascade genetic testing in the family members of BRCA1/2 gene pathogenic variant/likely pathogenic variant carriers. Sci Rep 2022; 12:1842. [PMID: 35115620 PMCID: PMC8813990 DOI: 10.1038/s41598-022-05931-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
The pathogenic variant (PV) or likely pathogenic variant (LPV) BRCA1/2 gene is strongly associated with hereditary breast or ovarian cancer. Therefore, it is important to screen blood relatives to establish preventive modalities and surveillance. This study evaluated the feasibility of targeted cascade genetic testing for family members of BRCA1/2 gene PV or LPV carriers. We screened 18 families for BRCA1/2 gene status via the conventional cascade genetic test (n = 9) and targeted cascade genetic test (n = 9), which targeted the exon region wherein the index patient showed PV or LPV. The pedigree and clinicopathologic characteristics were reviewed and analyzed. All index patients were diagnosed with breast cancer, while the third family members were all healthy. In the conventional cascade test group, 3 index patients and 3 family members had the BRCA1/2 gene PV or LPV. In the targeted cascade test group, 5 family members had same type of BRCA1/2 gene PV or LPV as their index patients. Two families had an identical string of BRCA1/2 gene PV or LPV. Although the targeted cascade genetic test cannot completely characterize the BRCA1/2 gene, it is sufficient for determining its PV or LPV status. This limited genetic test can be used for family members of PV or LPV carriers.
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Evaluation of Hereditary/Familial Breast Cancer Patients with Multigene Targeted Next Generation Sequencing Panel and MLPA Analysis in Turkey. Cancer Genet 2022; 262-263:118-133. [DOI: 10.1016/j.cancergen.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/20/2022] [Accepted: 02/15/2022] [Indexed: 11/18/2022]
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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18
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Li X, Wang Q, Wu Z, Zheng J, Ji L. Integrated Bioinformatics Analysis for Identification of the Hub Genes Linked with Prognosis of Ovarian Cancer Patients. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5113447. [PMID: 35047055 PMCID: PMC8763496 DOI: 10.1155/2022/5113447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND One of the most usual gynecological state of tumor is ovarian cancer and is a major reason of gynecological tumor-related global mortality rate. There have been multiple risk elements related to ovarian cancer like the background of past cases associated with breast cancer or ovarian cancer, or excessive body weight issues, case history of smoking, and untimely menstruation or menopause. Because of unclear expressions, more than 70% of the ovarian cancer patient cases are determined during the early stage. Material and Methods. GSE38666, GSE40595, and GSE66957 were the three microarray datasets which were analyzed using GEO2R for screening the differentially expressed genes. GO, Kyoto Encyclopedia of Genes, and protein expression studies were performed for analysis of hub genes. Then, survival analysis was performed for all the hub genes. RESULTS From the dataset, a total of 199 differentially expressed genes (DEGs) were identified. Through the KEGG pathway study, it was noted that the DEGs are mainly linked with the AGE-RAGE signaling pathway, central carbon metabolism, and human papillomavirus infection. The survival analysis showed 4 highly expressed hub genes COL4A1, SDC1, CDKN2A, and TOP2A which correlated with overall survival in ovarian cancer patients. Moreover, the expression of the 4 hub genes was validated by the GEPIA database and the Human Protein Atlas. CONCLUSION The results have shown that all 4 hub genes were found to be upregulated in ovarian cancer tissues which predict poor prognosis in patients with ovarian cancer.
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Affiliation(s)
- Xiaofeng Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qiu Wang
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhicheng Wu
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | | | - Ling Ji
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
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Zelli V, Compagnoni C, Capelli R, Corrente A, Cornice J, Vecchiotti D, Di Padova M, Zazzeroni F, Alesse E, Tessitore A. Emerging Role of isomiRs in Cancer: State of the Art and Recent Advances. Genes (Basel) 2021; 12:genes12091447. [PMID: 34573429 PMCID: PMC8469436 DOI: 10.3390/genes12091447] [Citation(s) in RCA: 3] [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: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
The advent of Next Generation Sequencing technologies brought with it the discovery of several microRNA (miRNA) variants of heterogeneous lengths and/or sequences. Initially ascribed to sequencing errors/artifacts, these isoforms, named isomiRs, are now considered non-canonical variants that originate from physiological processes affecting the canonical miRNA biogenesis. To date, accurate IsomiRs abundance, biological activity, and functions are not completely understood; however, the study of isomiR biology is an area of great interest due to their high frequency in the human miRNome, their putative functions in cooperating with the canonical miRNAs, and potential for exhibiting novel functional roles. The discovery of isomiRs highlighted the complexity of the small RNA transcriptional landscape in several diseases, including cancer. In this field, the study of isomiRs could provide further insights into the miRNA biology and its implication in oncogenesis, possibly providing putative new cancer diagnostic, prognostic, and predictive biomarkers as well. In this review, a comprehensive overview of the state of research on isomiRs in different cancer types, including the most common tumors such as breast cancer, colorectal cancer, melanoma, and prostate cancer, as well as in the less frequent tumors, as for example brain tumors and hematological malignancies, will be summarized and discussed.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Corrente
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Jessica Cornice
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Davide Vecchiotti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Monica Di Padova
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence: ; Tel.: +39-0862433518; Fax: +39-0862433131
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Ficarazzi F, Vecchi M, Ferrari M, Pierotti MA. Towards population-based genetic screenings for breast and ovarian cancer: A comprehensive review from economic evaluations to patient perspectives. Breast 2021; 58:121-129. [PMID: 34022715 PMCID: PMC8164087 DOI: 10.1016/j.breast.2021.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Genetic testing for hereditary breast and ovarian cancer following genetic counseling is based on guidelines that take into account particular features of the personal and family history, and clinical criteria conferring a probability of having a BRCA mutation greater than 10% as a threshold for accessing the test. However, besides reducing mortality and social impact, the extension of screening programs also for healthy family members would allow a huge saving of the rising costs associated with these pathologies, supporting the choice of the "Test" strategy versus a "No Test" one. Analyses of different health care systems show that by applying the "Test" strategy on patients and their families, a decrease in breast and ovarian cancer cases is achieved, as well as a substantial decrease in costs of economic resources, including the costs of the clinical management of early detected tumors. In this review, we analyzed the most recent papers published on this topic and we summarized the findings on the economic evaluations related to breast and ovarian cancer population screenings. These results proved and validated that the population-wide testing approach is a more accurate screening and preventive intervention than traditional guidelines based on personal/family history and clinical criteria to reduce breast and ovarian cancer risk.
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Affiliation(s)
| | - Manuela Vecchi
- Cogentech Ltd Benefit Corp, Via Adamello 16, 20139, Milan, Italy
| | - Maurizio Ferrari
- Cogentech Ltd Benefit Corp, Via Adamello 16, 20139, Milan, Italy; Vita-Salute San Raffaele University, Via Olgettina 58, 20132, Milan, Italy
| | - Marco A Pierotti
- Cogentech Ltd Benefit Corp, Via Adamello 16, 20139, Milan, Italy; IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy.
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21
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Zhao Y, Pi J, Liu L, Yan W, Ma S, Hong L. Identification of the Hub Genes Associated with the Prognosis of Ovarian Cancer Patients via Integrated Bioinformatics Analysis and Experimental Validation. Cancer Manag Res 2021; 13:707-721. [PMID: 33542655 PMCID: PMC7851396 DOI: 10.2147/cmar.s282529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/04/2020] [Indexed: 12/31/2022] Open
Abstract
Background This study aimed to identify the hub genes associated with prognosis of patients with ovarian cancer by using integrated bioinformatics analysis and experimental validation. Methods Four microarray datasets (GSE12470, GSE14407, GSE18521 and GSE46169) were analyzed by the GEO2R tool to screen common differentially expressed genes (DEGs). Gene Ontology, the Kyoto Encyclopedia of Genes and Genomes, the (KEGG) pathway and Reactome pathway enrichment analysis, protein–protein interaction (PPI) construction, and the identification of hub genes were performed. Furthermore, we performed the survival and expression analysis of the hub genes. In vitro functional assays were performed to assess the effects of hub genes on ovarian cancer cell proliferation, caspase-3/7 activity and invasion. Results A total of 89 common DEGs were identified among these four datasets. The KEGG and Reactome pathway results showed that the DEGs were mainly associated with cell cycle, mitotic and p53 signaling pathway. A total of 20 hub genes were identified from the PPI network by using sub-module analysis. The survival analysis revealed that high expression of six hub genes (AURKA, BUB1B, CENPF, KIF11, KIF23 and TOP2A) were significantly correlated with shorter overall survival and progression-free survival of patients with ovarian cancer. Furthermore, the expression of the six hub genes were validated by the GEPIA database and Human Protein Atlas, and functional studies revealed that knockdown of KIF11 and KIF23 suppressed the SKOV3 cell proliferation, increased caspase-3/7 activity and attenuated invasive potentials of SKOV3 cells. In addition, knockdown of KIF11 and KIF23 up-regulated E-cadherin mRNA expression but down-regulated N-cadherin and vimentin mRNA expression in SKOV3 cells. Conclusion Our results showed that six hub genes were up-regulated in ovarian cancer tissues and may predict poor prognosis of patients with ovarian cancer. KIF11 and KIF23 may play oncogenic roles in ovarian cancer cell progression via promoting ovarian cancer cell proliferation and invasion.
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Affiliation(s)
- Yuzi Zhao
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Jie Pi
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Lihua Liu
- Department of Gynaecology and Obstetrics, Huanggang Huangzhou Maternity and Child Health Care Hospital, Huanggang, People's Republic of China
| | - Wenjie Yan
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Shufang Ma
- Reproductive Medicine Center, Wuhan Kangjian Women and Infants Hospital, Wuhan, People's Republic of China
| | - Li Hong
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
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Pietragalla A, Arcieri M, Marchetti C, Scambia G, Fagotti A. Ovarian cancer predisposition beyond BRCA1 and BRCA2 genes. Int J Gynecol Cancer 2020; 30:1803-1810. [PMID: 32895312 DOI: 10.1136/ijgc-2020-001556] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Several genes associated with hereditary ovarian cancer have been discovered as a result of the work done with next generation sequencing. It is estimated that approximately 23% of ovarian carcinomas have a hereditary predisposition. The most common hereditary condition is represented by germline mutations in BRCA1 or BRCA2 genes that account for 20-25% of high grade serous ovarian cancer. A number of other hereditary ovarian cancers are associated with different genes, with a crucial role in the DNA damage response pathway, such as the mismatch repair genes in Lynch syndrome, TP53 in Li-Fraumeni syndrome, STK11 in Peutz-Jeghers syndrome, CHEK2, RAD51, BRIP1, and PALB2. The goal of this manuscript is to summarize the published data regarding the molecular pathways involved in the pathogenesis of non-BRCA related hereditary ovarian cancer and to provide a tool that might be useful in discussing risk assessment, genetic testing, prevention strategies, as well as clinical and therapeutic implications for patients with ovarian cancer.
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Affiliation(s)
- Antonella Pietragalla
- Department of Woman, Child, and Public Health, Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy
| | - Martina Arcieri
- Department of Obstetrics and Gynecology, University of Eastern Piedmont, Novara, Italy
| | - Claudia Marchetti
- Department of Woman, Child, and Public Health, Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy
| | - Giovanni Scambia
- Department of Woman, Child, and Public Health, Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy .,Catholic University of Sacred Heart, Rome, Italy
| | - Anna Fagotti
- Department of Woman, Child, and Public Health, Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy.,Catholic University of Sacred Heart, Rome, Italy
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