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Bhattarai S, Sugita BM, Bortoletto SM, Fonseca AS, Cavalli LR, Aneja R. QNBC Is Associated with High Genomic Instability Characterized by Copy Number Alterations and miRNA Deregulation. Int J Mol Sci 2021; 22:11548. [PMID: 34768979 PMCID: PMC8584247 DOI: 10.3390/ijms222111548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) can be further classified into androgen receptor (AR)-positive TNBC and AR-negative TNBC or quadruple-negative breast cancer (QNBC). Here, we investigated genomic instability in 53 clinical cases by array-CGH and miRNA expression profiling. Immunohistochemical analysis revealed that 64% of TNBC samples lacked AR expression. This group of tumors exhibited a higher level of copy number alterations (CNAs) and a higher frequency of cases affected by CNAs than TNBCs. CNAs in genes of the chromosome instability 25 (CIN25) and centrosome amplification (CA) signatures were more frequent in the QNBCs and were similar between the groups, respectively. However, expression levels of CIN25 and CA20 genes were higher in QNBCs. miRNA profiling revealed 184 differentially expressed miRNAs between the groups. Fifteen of these miRNAs were mapped at cytobands with CNAs, of which eight (miR-1204, miR-1265, miR-1267, miR-23c, miR-548ai, miR-567, miR-613, and miR-943), and presented concordance of expression and copy number levels. Pathway enrichment analysis of these miRNAs/mRNAs pairings showed association with genomic instability, cell cycle, and DNA damage response. Furthermore, the combined expression of these eight miRNAs robustly discriminated TNBCs from QNBCs (AUC = 0.946). Altogether, our results suggest a significant loss of AR in TNBC and a profound impact in genomic instability characterized by CNAs and deregulation of miRNA expression.
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Affiliation(s)
- Shristi Bhattarai
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
| | - Bruna M. Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
| | - Stefanne M. Bortoletto
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
| | - Aline S. Fonseca
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
| | - Luciane R. Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil; (B.M.S.); (S.M.B.); (A.S.F.)
- Lombardi Comprehensive Cancer Center, Oncology Department, Georgetown University, Washington, DC 20007, USA
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
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Silva JD, Nogueira L, Coelho R, Deus A, Khayat A, Marchi R, Oliveira ED, Santos APD, Cavalli L, Pereira S. HPV-associated penile cancer: Impact of copy number alterations in miRNA/mRNA interactions and potential druggable targets. Cancer Biomark 2021; 32:147-160. [PMID: 34151841 DOI: 10.3233/cbm-210035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Penile cancer (PeCa) is a rare disease, but its incidence has increased worldwide, mostly in HPV+ patients. Nevertheless, there is still no targeted treatment for this carcinoma. OBJECTIVE To predict the main signaling pathways involved in penile tumorigenesis and its potential drug targets. METHODS Genome-wide copy number profiling was performed in 28 PeCa. Integration analysis of CNAs and miRNAs and mRNA targets was performed by DIANA-TarBase v.8. The potential impact of the miRNAs/target genes on biological pathways was assessed by DIANA-miRPath v.3.0. For each miRNA, KEGG pathways were generated based on the tarbase and microT-CDS algorithms. Pharmaco-miR was used to identify associations between miRNAs and their target genes to predict druggable targets. RESULTS 269 miRNAs and 2,395 genes were mapped in cytobands with CNAs. The comparison of the miRNAs mapped at these cytobands and the miRNAs that were predicted to regulate the genes also mapped in these regions, resulted in a set of common 35 miRNAs and 292 genes. Enrichment pathway revealed their involvement in five top signaling pathways. EGFR and COX2 were identified as potential druggable targets. CONCLUSION Our data indicate the potential use of EGFR and COX2 inhibitors as a target treatment for PeCa patients.
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Affiliation(s)
- Jenilson da Silva
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, MA, Brazil
| | - Leudivan Nogueira
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, MA, Brazil.,Aldenora Bello Cancer Hospital, São Luís, MA, Brazil
| | - Ronald Coelho
- Aldenora Bello Cancer Hospital, São Luís, MA, Brazil
| | - Amanda Deus
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, MA, Brazil.,Aldenora Bello Cancer Hospital, São Luís, MA, Brazil
| | - André Khayat
- Oncology Research Center, Federal University of Pará, Belém, PA, Brazil
| | - Rafael Marchi
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Edivaldo de Oliveira
- Tissue Culture and Cytogenetics Laboratory, Institute of Evandro Chagas, Belém, PA, Brazil
| | - Ana Paula Dos Santos
- Department of Physiological Sciences, Federal University of Maranhão, São Luís, MA, Brazil
| | - Luciane Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Silma Pereira
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, MA, Brazil
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3
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Mathias C, Bortoletto S, Centa A, Komechen H, Lima RS, Fonseca AS, Sebastião AP, Urban CA, Soares EWS, Prando C, Figueiredo BC, Cavalli IJ, Cavalli LR, Ribeiro EMFS. Frequency of the TP53 R337H variant in sporadic breast cancer and its impact on genomic instability. Sci Rep 2020; 10:16614. [PMID: 33024147 PMCID: PMC7539008 DOI: 10.1038/s41598-020-73282-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/17/2020] [Indexed: 01/25/2023] Open
Abstract
The R337H is a TP53 germline pathogenic variant that has been associated with several types of cancers, including breast cancer. Our main objective was to determine the frequency of the R337H variant in sporadic breast cancer patients from Paraná state, South Brazil, its association with prognosis and its impact in genomic instability. The genotyping of 805 breast cancer tissues revealed a genotypic and allelic frequency of the R337H variant of 2.36% and 1.18%, respectively. In these R337H+ cases a lower mean age at diagnosis was observed when compared to the R337H-cases. Array-CGH analysis showed that R337H+ patients presented a higher number of copy number alterations (CNAs), compared to the R337H−. These CNAs affected genes and miRNAs that regulate critical cancer signaling pathways; a number of these genes were associated with survival after querying the KMplot database. Furthermore, homozygous (R337H+/R337H+) fibroblasts presented increased levels of copy number variants when compared to heterozygous or R337H− cells. In conclusion, the R337H variant may contribute to 2.36% of the breast cancer cases without family cancer history in Paraná. Among other mechanisms, R337H increases the level of genomic instability, as evidenced by a higher number of CNAs in the R337H+ cases compared to the R337H−.
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Affiliation(s)
- Carolina Mathias
- Graduate Program of Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Paraná, 81531980, Brazil
| | - Stéfanne Bortoletto
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, 80250060, Brazil
| | - Ariana Centa
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, 80250060, Brazil
| | - Heloisa Komechen
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, 80250060, Brazil
| | - Rubens S Lima
- Breast Disease Center, Hospital Nossa Senhora das Graças, Curitiba, Paraná, 80810040, Brazil
| | - Aline S Fonseca
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, 80250060, Brazil
| | - Ana Paula Sebastião
- Department of Pathology, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, 81531980, Brazil.,Service of Pathology, Hospital Nossa Senhora das Graças, Curitiba, Paraná, 80810040, Brazil
| | - Cícero A Urban
- Breast Disease Center, Hospital Nossa Senhora das Graças, Curitiba, Paraná, 80810040, Brazil
| | - Emerson W S Soares
- União Oeste Paranaense de Estudos E Combate Ao Câncer, Cascavel, Paraná, 85806300, Brazil
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, 80250060, Brazil
| | - Bonald C Figueiredo
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, 80250060, Brazil
| | - Iglenir J Cavalli
- Graduate Program of Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Paraná, 81531980, Brazil
| | - Luciane R Cavalli
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, 80250060, Brazil. .,Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20007, USA.
| | - Enilze M F S Ribeiro
- Graduate Program of Genetics, Department of Genetics, Federal University of Paraná, Curitiba, Paraná, 81531980, Brazil
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Zhu Y, Dong S, Zhu Y, Zhao Y, Xu Y. Identification of cancer prognosis-associated lncRNAs based on the miRNA-TF co-regulatory motifs and dosage sensitivity. Mol Omics 2019; 15:361-373. [DOI: 10.1039/c9mo00089e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
By integrating dosage sensitivity and motif regulation data, we established a framework and identified a total of 33 cancer prognosis-associated lncRNAs.
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Affiliation(s)
- Yinling Zhu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Siyao Dong
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Yanjiao Zhu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Yichuan Zhao
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Yan Xu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
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5
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Soh J, Cho H, Choi CH, Lee H. Identification and Characterization of MicroRNAs Associated with Somatic Copy Number Alterations in Cancer. Cancers (Basel) 2018; 10:cancers10120475. [PMID: 30501131 PMCID: PMC6315597 DOI: 10.3390/cancers10120475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/10/2018] [Accepted: 11/24/2018] [Indexed: 12/30/2022] Open
Abstract
MicroRNAs (miRNAs) are key molecules that regulate biological processes such as cell proliferation, differentiation, and apoptosis in cancer. Somatic copy number alterations (SCNAs) are common genetic mutations that play essential roles in cancer development. Here, we investigated the association between miRNAs and SCNAs in cancer. We collected 2538 tumor samples for seven cancer types from The Cancer Genome Atlas. We found that 32−84% of miRNAs are in SCNA regions, with the rate depending on the cancer type. In these regions, we identified 80 SCNA-miRNAs whose expression was mainly associated with SCNAs in at least one cancer type and showed that these SCNA-miRNAs are related to cancer by survival analysis and literature searching. We also identified 58 SCNA-miRNAs common in the seven cancer types (CC-SCNA-miRNAs) and showed that these CC-SCNA-miRNAs are more likely to be related with protein and gene expression than other miRNAs. Furthermore, we experimentally validated the oncogenic role of miR-589. In conclusion, our results suggest that SCNA-miRNAs significantly alter biological processes related to cancer development, confirming the importance of SCNAs in non-coding regions in cancer.
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Affiliation(s)
- Jihee Soh
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju 61005, Korea.
| | - Hyejin Cho
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju 61005, Korea.
| | - Chan-Hun Choi
- College of Korean Medicine, Dongshin University, Naju-si, Jeollanam-do 58245, Korea.
| | - Hyunju Lee
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, Gwangju 61005, Korea.
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6
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Liu Y, Zhang R, Zhao N, Zhang Q, Yan Z, Chang Z, Wei Y, Wu C, Xu J, Xu Y. A comparative analysis reveals the dosage sensitivity and regulatory patterns of lncRNA in prostate cancer. MOLECULAR BIOSYSTEMS 2016; 12:3176-85. [PMID: 27507663 DOI: 10.1039/c6mb00359a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although the key roles of long non-coding RNAs (lncRNAs) in multiple diseases are well documented, the relationship between the lncRNA copy number and expression is unknown. Here, we present a comprehensive study that demonstrates the impact of miRNA-TF co-regulatory motifs on the dosage effects of protein-coding genes (PCGs) and lncRNAs in prostate cancer. By integrating copy number profiles, expression profiles and regulatory relationships with miRNAs and transcription factors, we reveal that lncRNAs and PCGs correlate with distinct dosage sensitivity and regulatory pattern characteristics. We also show that lncRNAs from different genomic regions have different features. Using a custom-built framework, we identified 24 candidate prostate cancer-related lncRNAs based on the known properties of established prostate-related lncRNAs. Our method will enable the identification of cancer-related lncRNAs, which will provide new insights into cancer lncRNA biology.
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Affiliation(s)
- Yongjing Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Klonowska K, Czubak K, Wojciechowska M, Handschuh L, Zmienko A, Figlerowicz M, Dams-Kozlowska H, Kozlowski P. Oncogenomic portals for the visualization and analysis of genome-wide cancer data. Oncotarget 2016; 7:176-92. [PMID: 26484415 PMCID: PMC4807991 DOI: 10.18632/oncotarget.6128] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/28/2015] [Indexed: 12/27/2022] Open
Abstract
Somatically acquired genomic alterations that drive oncogenic cellular processes are of great scientific and clinical interest. Since the initiation of large-scale cancer genomic projects (e.g., the Cancer Genome Project, The Cancer Genome Atlas, and the International Cancer Genome Consortium cancer genome projects), a number of web-based portals have been created to facilitate access to multidimensional oncogenomic data and assist with the interpretation of the data. The portals provide the visualization of small-size mutations, copy number variations, methylation, and gene/protein expression data that can be correlated with the available clinical, epidemiological, and molecular features. Additionally, the portals enable to analyze the gathered data with the use of various user-friendly statistical tools. Herein, we present a highly illustrated review of seven portals, i.e., Tumorscape, UCSC Cancer Genomics Browser, ICGC Data Portal, COSMIC, cBioPortal, IntOGen, and BioProfiling.de. All of the selected portals are user-friendly and can be exploited by scientists from different cancer-associated fields, including those without bioinformatics background. It is expected that the use of the portals will contribute to a better understanding of cancer molecular etiology and will ultimately accelerate the translation of genomic knowledge into clinical practice.
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Affiliation(s)
- Katarzyna Klonowska
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Karol Czubak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marzena Wojciechowska
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Luiza Handschuh
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Agnieszka Zmienko
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Sciences, Poznan University of Technology, Poznan, Poland
| | - Marek Figlerowicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Sciences, Poznan University of Technology, Poznan, Poland
| | - Hanna Dams-Kozlowska
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Kozlowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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