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Almohaywi M, Sugita BM, Centa A, Fonseca AS, Antunes VC, Fadda P, Mannion CM, Abijo T, Goldberg SL, Campbell MC, Copeland RL, Kanaan Y, Cavalli LR. Deregulated miRNA Expression in Triple-Negative Breast Cancer of Ancestral Genomic-Characterized Latina Patients. Int J Mol Sci 2023; 24:13046. [PMID: 37685851 PMCID: PMC10487916 DOI: 10.3390/ijms241713046] [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: 06/29/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 09/10/2023] Open
Abstract
Among patients with triple-negative breast cancer (TNBC), several studies have suggested that deregulated microRNA (miRNA) expression may be associated with a more aggressive phenotype. Although tumor molecular signatures may be race- and/or ethnicity-specific, there is limited information on the molecular profiles in women with TNBC of Hispanic and Latin American ancestry. We simultaneously profiled TNBC biopsies for the genome-wide copy number and miRNA global expression from 28 Latina women and identified a panel of 28 miRNAs associated with copy number alterations (CNAs). Four selected miRNAs (miR-141-3p, miR-150-5p, miR-182-5p, and miR-661) were validated in a subset of tumor and adjacent non-tumor tissue samples, with miR-182-5p being the most discriminatory among tissue groups (AUC value > 0.8). MiR-141-3p up-regulation was associated with increased cancer recurrence; miR-661 down-regulation with larger tumor size; and down-regulation of miR-150-5p with larger tumor size, high p53 expression, increased cancer recurrence, presence of distant metastasis, and deceased status. This study reinforces the importance of integration analysis of CNAs and miRNAs in TNBC, allowing for the identification of interactions among molecular mechanisms. Additionally, this study emphasizes the significance of considering the patients ancestral background when examining TNBC, as it can influence the relationship between intrinsic tumor molecular characteristics and clinical manifestations of the disease.
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Affiliation(s)
- Maram Almohaywi
- Microbiology Department, Howard University Cancer Center, Howard University, Washington, DC 20059, USA
| | - Bruna M. Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, PR, Brazil
| | - Ariana Centa
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, PR, Brazil
| | - Aline S. Fonseca
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, PR, Brazil
| | - Valquiria C. Antunes
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, PR, Brazil
| | - Paolo Fadda
- Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Ciaran M. Mannion
- Department of Pathology, Hackensack University Medical Center, Hackensack, NJ 07701, USA
| | - Tomilowo Abijo
- National Institute of Diabetes and Kidney Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | - Stuart L. Goldberg
- John Theurer Cancer Center, Hackensack Meridian School of Medicine, Hackensack, NJ 07701, USA
- COTA, Inc., New York, NY 10014, USA
| | - Michael C. Campbell
- Department of Biological Sciences Human and Evolutionary Biology Section, University of Southern California, Los Angeles, CA 90089, USA
| | - Robert L. Copeland
- Pharmacology Department, Howard University Cancer Center, Howard University, Washington, DC 20059, USA
| | - Yasmine Kanaan
- Microbiology Department, Howard University Cancer Center, Howard University, Washington, DC 20059, USA
| | - Luciane R. Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, PR, Brazil
- Oncology Department, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
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2
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Gradowski Farias da Costa do Nascimento T, de Oliveira Thomazini ME, de França Junior N, de Castro Poncio L, Fonseca AS, de Figueiredo BC, Weber SH, Herai RH, de Noronha L, Cavalli LR, Feltes BC, Elifio-Esposito S. Systems biology network reveals the correlation between COX-2 expression and Ch 7q copy number alterations in Ch 11q-deleted pediatric neuroblastoma tumors. Genes Cancer 2022; 13:60-71. [PMCID: PMC9718587 DOI: 10.18632/genesandcancer.225] [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: 06/02/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
Tumor-associated inflammation and chromosomal aberrations can play crucial roles in cancer development and progression. In neuroblastoma (NB), the enzyme cyclooxygenase-2 (COX-2) is associated with copy number alterations on the long arm of chromosome 11 (Ch 11q), defining an aggressive disease subset. This retrospective study included formalin-fixed paraffin-embedded tumor samples collected from nine patients during diagnosis at the pediatric Pequeno Principe Hospital, Curitiba, PR, Brazil, and post-chemotherapy (CT). COX-2 expression was evaluated using immunohistochemistry and correlated with the genome profile of paired pre- and post-CT samples, determined by array comparative genomic hybridization. A systems biology approach elucidated the PTGS2 network interaction. The results showed positive correlations between pre-CT Ch 7q gain and COX-2 expression (ρ = 0.825; p-value = 0.006) and negative correlations between Ch 7q gain and Ch 11q deletion (ρ = −0.919; p-value = 0.0005). Three samples showed Ch 11q deletion and Ch 7q gain. Network analysis identified a direct connection between CAV-1 (Ch 7q) and COX-2 in NB tumors and highlighted the connection between amplified genes in Ch 7q and deleted ones in 11q. The identification of hub-bottleneck-switch genes provides new biological insights into this connection between NB, tumorigenesis, and inflammation.
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Affiliation(s)
| | - Mateus Eduardo de Oliveira Thomazini
- 1Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil,2Biotechnology Undergraduate Program. School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Nilton de França Junior
- 1Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | | | - Aline Simoneti Fonseca
- 3Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | | | - Saulo Henrique Weber
- 4Graduate Program in Animal Science, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Roberto Hirochi Herai
- 1Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil,5Research Department, Instituto Buko Kaesemodel (IBK), Curitiba, Paraná, Brazil
| | - Lucia de Noronha
- 1Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Luciane R. Cavalli
- 3Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil,6Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Bruno César Feltes
- 7Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil,8Institute of Biosciences, Department of Biophysics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Selene Elifio-Esposito
- 1Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil,Correspondence to:Selene Elifio-Esposito, email:
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3
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Sugita BM, Rodriguez Y, Fonseca AS, Nunes Souza E, Kallakury B, Cavalli IJ, Ribeiro EMSF, Aneja R, Cavalli LR. MiR-150-5p Overexpression in Triple-Negative Breast Cancer Contributes to the In Vitro Aggressiveness of This Breast Cancer Subtype. Cancers (Basel) 2022; 14:cancers14092156. [PMID: 35565284 PMCID: PMC9104497 DOI: 10.3390/cancers14092156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 01/16/2023] Open
Abstract
Simple Summary Triple-negative breast cancer (TNBC) is a clinically aggressive type of breast cancer. MicroRNAs (miRNAs) are small molecules that regulate the expression of genes involved in tumor cell signaling. The miR-150-5p is frequently deregulated in cancer, with expression and mode of action varying according to the cancer type. In this study, we investigated the expression levels of miR-150-5p in TNBC, its association with clinical and pathological features of patients, and its role in modulating TNBC cell proliferation, migration, and drug resistance. Our results suggest that miR-150-5p is highly expressed in TNBC and that miR-150-5p expression levels are associated with tumor grade, patient survival, and ethnicity. Our findings also indicate that miR-150-5p contributes to the aggressive phenotypes of TNBC cells in vitro. Abstract MiR-150-5p is frequently deregulated in cancer, with expression and mode of action varying according to the tumor type. Here, we investigated the expression levels and role of miR-150-5p in the aggressive breast cancer subtype triple-negative breast cancer (TNBC). MiR-150-5p expression levels were analyzed in tissue samples from 113 patients with invasive breast cancer (56 TNBC and 57 non-TNBC) and 41 adjacent non-tumor tissues (ANT). Overexpression of miR-150-5p was observed in tumor tissues compared with ANT tissues and in TNBC compared with non-TNBC tissues. MiR-150-5p expression levels were significantly associated with high tumor grades and the Caucasian ethnicity. Interestingly, high miR-150-5p levels were associated with prolonged overall survival. Manipulation of miR-150-5p expression in TNBC cells modulated cell proliferation, clonogenicity, migration, and drug resistance. Manipulation of miR-150-5p expression also resulted in altered expression of its mRNA targets, including epithelial-to-mesenchymal transition markers, MYB, and members of the SRC pathway. These findings suggest that miR-150-5p is overexpressed in TNBC and contributes to the aggressiveness of TNBC cells in vitro.
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Affiliation(s)
- Bruna M. Sugita
- Research Institute Pele Pequeno Príncipe, Faculdades Pequeno Príncipe Curitiba, Curitiba 80250-060, Brazil; (B.M.S.); (A.S.F.); (E.N.S.)
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA;
- Genetics Post-Graduation Program, Department of Genetics, Federal University of Paraná, Curitiba 81530-000, Brazil; (I.J.C.); (E.M.S.F.R.)
| | - Yara Rodriguez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA;
| | - Aline S. Fonseca
- Research Institute Pele Pequeno Príncipe, Faculdades Pequeno Príncipe Curitiba, Curitiba 80250-060, Brazil; (B.M.S.); (A.S.F.); (E.N.S.)
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA;
| | - Emanuelle Nunes Souza
- Research Institute Pele Pequeno Príncipe, Faculdades Pequeno Príncipe Curitiba, Curitiba 80250-060, Brazil; (B.M.S.); (A.S.F.); (E.N.S.)
| | - Bhaskar Kallakury
- Department of Pathology, Georgetown University Medical Center, Washington, DC 20007, USA;
| | - Iglenir J. Cavalli
- Genetics Post-Graduation Program, Department of Genetics, Federal University of Paraná, Curitiba 81530-000, Brazil; (I.J.C.); (E.M.S.F.R.)
| | - Enilze M. S. F. Ribeiro
- Genetics Post-Graduation Program, Department of Genetics, Federal University of Paraná, Curitiba 81530-000, Brazil; (I.J.C.); (E.M.S.F.R.)
| | - Ritu Aneja
- Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Luciane R. Cavalli
- Research Institute Pele Pequeno Príncipe, Faculdades Pequeno Príncipe Curitiba, Curitiba 80250-060, Brazil; (B.M.S.); (A.S.F.); (E.N.S.)
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA;
- Correspondence:
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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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5
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DLX Genes: Roles in Development and Cancer. Cancers (Basel) 2021; 13:cancers13123005. [PMID: 34203994 PMCID: PMC8232755 DOI: 10.3390/cancers13123005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary DLX homeobox family genes encode transcription factors that have indispensable roles in embryonic and postnatal development. These genes are critically linked to the morphogenesis of craniofacial structures, branchial arches, forebrain, and sensory organs. DLX genes are also involved in postnatal homeostasis, particularly hematopoiesis and, when dysregulated, oncogenesis. DLX1/2, DLX3/4, and DLX5/6 exist as bigenes on different chromosomes, sharing intergenic enhancers between gene pairs, which allows orchestrated spatiotemporal expression. Genomic alterations of human DLX gene enhancers or coding sequences result in congenital disorders such as split-hand/foot malformation. Aberrant postnatal expression of DLX genes is associated with hematological malignancies, including leukemias and lymphomas. In several mouse models of T-cell lymphoma, Dlx5 has been shown to act as an oncogene by cooperating with activated Akt, Notch1/3, and/or Wnt to drive tumor formation. In humans, DLX5 is aberrantly expressed in lung and ovarian carcinomas and holds promise as a therapeutic target. Abstract Homeobox genes control body patterning and cell-fate decisions during development. The homeobox genes consist of many families, only some of which have been investigated regarding a possible role in tumorigenesis. Dysregulation of HOX family genes have been widely implicated in cancer etiology. DLX homeobox genes, which belong to the NK-like family, exert dual roles in development and cancer. The DLX genes are the key transcription factors involved in regulating the development of craniofacial structures in vertebrates. The three DLX bigenes have overlapping expression in the branchial arches. Disruption of DLX function has destructive consequences in organogenesis and is associated with certain congenital disorders in humans. The role of DLX genes in oncogenesis is only beginning to emerge. DLX2 diminishes cellular senescence by regulating p53 function, whereas DLX4 has been associated with metastasis in breast cancer. In human ovarian cancer cells, DLX5 is essential for regulating AKT signaling, thereby promoting cell proliferation and survival. We previously implicated Dlx5 as an oncogene in murine T-cell lymphoma driven by a constitutively active form of Akt2. In this mouse model, overexpression of Dlx5 was caused by a chromosomal rearrangement that juxtaposed the Tcr-beta promoter region near the Dlx5 locus. Moreover, transgenic mice overexpressing Dlx5, specifically in immature T-cells, develop spontaneous thymic lymphomas. Oncogenesis in this mouse model involves binding of Dlx5 to the Notch1 and Notch3 gene loci to activate their transcription. Dlx5 also cooperates with Akt signaling to accelerate lymphomagenesis by activating Wnt signaling. We also discuss the fact that human DLX5 is aberrantly expressed in several human malignancies.
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6
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Rodrigues MFSD, Xavier FCA, Esteves CD, Nascimento RB, Nobile JS, Severino P, de Cicco R, Toporcov TN, Tajara EH, Nunes FD. Homeobox gene amplification and methylation in oral squamous cell carcinoma. Arch Oral Biol 2021; 129:105195. [PMID: 34126417 DOI: 10.1016/j.archoralbio.2021.105195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Investigate the DNA copy number and the methylation profile of the homeobox genes HOXA5, HOXA7, HOXA9, HOXB5, HOXB13, HOXC12, HOXC13, HOXD10, HOXD11, IRX4 and ZHX1, and correlate them with clinicopathological parameters and overall survival. MATERIAL AND METHODS DNA from OSCC samples and surgical margins were submitted to DNA amplification by qPCR and to DNA methylation analysis using a DNA Methylation PCR Array System. RESULTS HOXA5, HOXB5 and HOXD10 were amplified in surgical margins while HOXA9, HOXB13 and IRX4 were amplified in OSCC. HOXD10 demonstrated hypermethylation in half of the tumor while ZHX1 did not show hypermethylation. No correlation of DNA copy number or methylation with clinicopathological parameters or survival was observed. CONCLUSION HOXA9, HOXB13 and IRX4 genes appears to be regulated by amplification and HOXD10 by methylation in OSCC. Further studies are needed to determine the role of these events in OSCC development.
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Affiliation(s)
| | - Flávia Caló Aquino Xavier
- Laboratory of Oral Surgical Pathology, School of Dentistry, Federal University of Bahia, Salvador, Brazil
| | - Carina Duarte Esteves
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Rebeca Barros Nascimento
- Laboratory of Oral Surgical Pathology, School of Dentistry, Federal University of Bahia, Salvador, Brazil
| | - Juliana Stephan Nobile
- Postgraduate Program in Biophotonics Applied to Health Sciences, Nove De Julho University (UNINOVE), São Paulo, SP, Brazil
| | - Patrícia Severino
- Center for Experimental Research, Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo, Brazil
| | | | | | - Eloiza Helena Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Fábio Daumas Nunes
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil.
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7
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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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Wang Z, Zhang L, He L, Cui D, Liu C, Yin L, Zhang M, Jiang L, Gong Y, Wu W, Liu B, Li X, Cram DS, Liu D. Low-depth whole genome sequencing reveals copy number variations associated with higher pathologic grading and more aggressive subtypes of lung non-mucinous adenocarcinoma. Chin J Cancer Res 2020; 32:334-346. [PMID: 32694898 PMCID: PMC7369181 DOI: 10.21147/j.issn.1000-9604.2020.03.05] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Objective Histology grade, subtypes and TNM stage of lung adenocarcinomas are useful predictors of prognosis and survival. The aim of the study was to investigate the relationship between chromosomal instability, morphological subtypes and the grading system used in lung non-mucinous adenocarcinoma (LNMA). Methods We developed a whole genome copy number variation (WGCNV) scoring system and applied next generation sequencing to evaluate CNVs present in 91 LNMA tumor samples. Results Higher histological grades, aggressive subtypes and more advanced TNM staging were associated with an increased WGCNV score, particularly in CNV regions enriched for tumor suppressor genes and oncogenes. In addition, we demonstrate that 24-chromosome CNV profiling can be performed reliably from specific cell types (<100 cells) isolated by sample laser capture microdissection. Conclusions Our findings suggest that the WGCNV scoring system we developed may have potential value as an adjunct test for predicting the prognosis of patients diagnosed with LNMA.
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Affiliation(s)
- Zheng Wang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Lin Zhang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Lei He
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Di Cui
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Chenglong Liu
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Liangyu Yin
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Min Zhang
- Department of Radiology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Lei Jiang
- Department of Radiology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Yuyan Gong
- Berry Genomics Corporation, Beijing 102206, China
| | - Wang Wu
- Berry Genomics Corporation, Beijing 102206, China
| | - Bi Liu
- Berry Genomics Corporation, Beijing 102206, China
| | - Xiaoyu Li
- Berry Genomics Corporation, Beijing 102206, China
| | - David S Cram
- Berry Genomics Corporation, Beijing 102206, China
| | - Dongge Liu
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing 100730, China
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9
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Sugita BM, Pereira SR, de Almeida RC, Gill M, Mahajan A, Duttargi A, Kirolikar S, Fadda P, de Lima RS, Urban CA, Makambi K, Madhavan S, Boca SM, Gusev Y, Cavalli IJ, Ribeiro EMSF, Cavalli LR. Integrated copy number and miRNA expression analysis in triple negative breast cancer of Latin American patients. Oncotarget 2019; 10:6184-6203. [PMID: 31692930 PMCID: PMC6817452 DOI: 10.18632/oncotarget.27250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
Triple negative breast cancer (TNBC), a clinically aggressive breast cancer subtype, affects 15–35% of women from Latin America. Using an approach of direct integration of copy number and global miRNA profiling data, performed simultaneously in the same tumor specimens, we identified a panel of 17 miRNAs specifically associated with TNBC of ancestrally characterized patients from Latin America, Brazil. This panel was differentially expressed between the TNBC and non-TNBC subtypes studied (p ≤ 0.05, FDR ≤ 0.25), with their expression levels concordant with the patterns of copy number alterations (CNAs), present mostly frequent at 8q21.3-q24.3, 3q24-29, 6p25.3-p12.2, 1q21.1-q44, 5q11.1-q22.1, 11p13-p11.2, 13q12.11-q14.3, 17q24.2-q25.3 and Xp22.33-p11.21. The combined 17 miRNAs presented a high power (AUC = 0.953 (0.78–0.99);95% CI) in discriminating between the TNBC and non-TNBC subtypes of the patients studied. In addition, the expression of 14 and 15 of the 17miRNAs was significantly associated with tumor subtype when adjusted for tumor stage and grade, respectively. In conclusion, the panel of miRNAs identified demonstrated the impact of CNAs in miRNA expression levels and identified miRNA target genes potentially affected by both CNAs and miRNA deregulation. These targets, involved in critical signaling pathways and biological functions associated specifically with the TNBC transcriptome of Latina patients, can provide biological insights into the observed differences in the TNBC clinical outcome among racial/ethnic groups, taking into consideration their genetic ancestry.
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Affiliation(s)
- Bruna M Sugita
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil.,Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
| | - Silma R Pereira
- Department of Biology, Federal University of Maranhão, São Luis, MA, Brazil
| | - Rodrigo C de Almeida
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, Netherlands
| | - Mandeep Gill
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Akanksha Mahajan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Anju Duttargi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Saurabh Kirolikar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Paolo Fadda
- Genomics Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rubens S de Lima
- Breast Unit, Hospital Nossa Senhora das Graças, Curitiba, PR, Brazil
| | - Cicero A Urban
- Breast Unit, Hospital Nossa Senhora das Graças, Curitiba, PR, Brazil
| | - Kepher Makambi
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington DC, USA
| | - Subha Madhavan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA.,Innovation Center for Biomedical Informatics (ICBI), Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Simina M Boca
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA.,Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington DC, USA.,Innovation Center for Biomedical Informatics (ICBI), Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Yuriy Gusev
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA.,Innovation Center for Biomedical Informatics (ICBI), Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Iglenir J Cavalli
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil
| | | | - Luciane R Cavalli
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil.,Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
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10
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Zhang L, Wan Y, Jiang Y, Zhang Z, Shu S, Cheng W, Lang J. Overexpression of BP1, an isoform of Homeobox Gene DLX4, promotes cell proliferation, migration and predicts poor prognosis in endometrial cancer. Gene 2019; 707:216-223. [PMID: 31100338 DOI: 10.1016/j.gene.2019.05.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 01/13/2023]
Abstract
The expression of homeobox gene DLX4 has been verified in some tumors, but not in endometrial cancer. We found that expression of DLX7, a splicing isoform of DLX4, did not show any significant difference in expression between endometrial cancer and endometrium. However, BP1, another splicing isoform of DLX4, was highly expressed in endometrial cancer, and its expression was positively correlated with patient prognosis, cancer pathological grade, tumor invasion and metastasis. Lentiviral-mediated expression of BP1 in HEC-1-B cells accelerated the cell cycle progression from G0/G1 into S phase, and promoted cell proliferation and migration both in vitro and in vivo. Real-time PCR and western blotting showed that the expression levels of p15, p21 and E-cadherin significantly decreased, and levels of cyclinD1 and MMP-2 increased in endometrial cancer cells. In conclusion, our results demonstrate that high expression of BP1 is associated with poor prognosis in patients with endometrial cancer and promotes cell proliferation and migration.
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Affiliation(s)
- Lin Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Yicong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China.
| | - Zihan Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China.
| | - Shan Shu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu 210029, China.
| | - Jinghe Lang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China.
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11
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Lupicki K, Elifio-Esposito S, Fonseca AS, Weber SH, Sugita B, Langa BC, Pereira SRF, Govender D, Panieri E, Hiss DC, Abdul-Rasool S, Cavalli LR. Patterns of copy number alterations in primary breast tumors of South African patients and their impact on functional cellular pathways. Int J Oncol 2018; 53:2745-2757. [PMID: 30320392 DOI: 10.3892/ijo.2018.4589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/24/2018] [Indexed: 11/05/2022] Open
Abstract
Breast cancer is the most common and the leading cause of female mortality among South African (SA) women. Several non‑biological and biological risk factors may be attributed to their observed high mortality rate; however, the molecular profiles associated with their breast tumors are poorly characterized. The present study examined the patterns of genome-wide copy number alterations (CNAs) and their potential impact on functional cellular pathways targeted by cancer driver genes in patients with breast cancer from the Western Cape region of SA. Array-comparative genomic hybridization analysis, performed in 28 cases of invasive breast cancer, revealed a mean number of 8.68±6.18 CNAs per case, affecting primarily the Xp22.3 and 6p21-p25 cytobands (57.14% of the cases), followed by 19p13.3-p13.11 (35.7%), 2p25.3-p24.3, 4p16.3-p15.3, 8q11.1-q24.3 and 16 p13.3-p11.2 (32.14%). Functional enrichment analysis of genes and microRNA targets mapped in these affected cytobands revealed critical cancer-associated pathways, including fatty acid biosynthesis and metabolism, extracellular matrix-receptor interaction, hippo and tumor protein p53 signaling pathways, which are regulated by known cancer genes, including CCND1, CDKN1A, MAPK1, MDM2, TP53 and SMAD2. An inverse correlation was observed among the number of CNAs and tumor size and grade; CNAs on the 4p and 6p cytobands were also inversely correlated with tumor grade. No association was observed in the number of CNAs and/or the affected cytobands and the different ethnic groups of the SA patients, indicating that their tumor genome is affected by CNAs, irrespectively of their genetic descent. Additional genomic tumor profiling in SA and other Sub-Saharan African patients with breast cancer is required to determine the associations of the CNAs observed with prognosis and clinical outcome.
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Affiliation(s)
- Kamil Lupicki
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC 20007, USA
| | - Selene Elifio-Esposito
- Department of Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil
| | - Aline S Fonseca
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC 20007, USA
| | - Saulo H Weber
- Department of Biotechnology, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil
| | - Bruna Sugita
- Department of Genetics, Federal University of Parana, Curitiba, Paraná 80060-000, Brazil
| | - Bridget C Langa
- Department of Medical Biosciences, University of the Western Cape, Bellville, Western Cape 7535, South Africa
| | - Silma R F Pereira
- Department of Biology, Federal University of Maranhão, São Luis, Maranhão 65080-805, Brazil
| | - Dhirendra Govender
- Division of Anatomical Pathology, University of Cape Town, National Health Laboratory Service, Groote Schuur Hospital, Cape Town 7700, South Africa
| | - Eugene Panieri
- Department of Surgical Oncology, Groote Schuur Hospital, Cape Town 7700, South Africa
| | - Donavon C Hiss
- Department of Medical Biosciences, University of the Western Cape, Bellville, Western Cape 7535, South Africa
| | - Sahar Abdul-Rasool
- Department of Medical Biosciences, University of the Western Cape, Bellville, Western Cape 7535, South Africa
| | - Luciane R Cavalli
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC 20007, USA
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12
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Stires H, Heckler MM, Fu X, Li Z, Grasso CS, Quist MJ, Lewis JA, Klimach U, Zwart A, Mahajan A, Győrffy B, Cavalli LR, Riggins RB. Integrated molecular analysis of Tamoxifen-resistant invasive lobular breast cancer cells identifies MAPK and GRM/mGluR signaling as therapeutic vulnerabilities. Mol Cell Endocrinol 2018; 471:105-117. [PMID: 28935545 PMCID: PMC5858970 DOI: 10.1016/j.mce.2017.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/26/2017] [Accepted: 09/15/2017] [Indexed: 12/13/2022]
Abstract
Invasive lobular breast cancer (ILC) is an understudied malignancy with distinct clinical, pathological, and molecular features that distinguish it from the more common invasive ductal carcinoma (IDC). Mounting evidence suggests that estrogen receptor-alpha positive (ER+) ILC has a poor response to Tamoxifen (TAM), but the mechanistic drivers of this are undefined. In the current work, we comprehensively characterize the SUM44/LCCTam ILC cell model system through integrated analysis of gene expression, copy number, and mutation, with the goal of identifying actionable alterations relevant to clinical ILC that can be co-targeted along with ER to improve treatment outcomes. We show that TAM has several distinct effects on the transcriptome of LCCTam cells, that this resistant cell model has acquired copy number alterations and mutations that impinge on MAPK and metabotropic glutamate receptor (GRM/mGluR) signaling networks, and that pharmacological inhibition of either improves or restores the growth-inhibitory actions of endocrine therapy.
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Affiliation(s)
- Hillary Stires
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Mary M Heckler
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Xiaoyong Fu
- Lester and Sue Smith Breast Center, Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Zhao Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | - Joseph A Lewis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Uwe Klimach
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Alan Zwart
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Akanksha Mahajan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Luciane R Cavalli
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Rebecca B Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
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13
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Jeong J, Naab TJ, Fernandez AI, Ongkeko MS, Makambi KH, Blancato JK. Homeoprotein DLX4 expression is increased in inflammatory breast cancer cases from an urban African-American population. Oncotarget 2018; 9:31253-31263. [PMID: 30131852 PMCID: PMC6101289 DOI: 10.18632/oncotarget.25790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/05/2018] [Indexed: 02/07/2023] Open
Abstract
Protein expression of Distal-less homeobox 4 (DLX4) was analyzed in inflammatory breast cancer (IBC) cases from an African-American (AA) population to determine if a) DLX4 gene over expression exists in this cohort and b) if the overexpression is associated with breast cancer clinicopathological characteristics (ER, PR, HER2, triple-negative). Twenty-nine blocks of formalin-fixed paraffin-embedded (FFPE) tissue from well-characterized human IBC cases were used for immunohistochemical staining (IHC). IHC results were assigned an intensity and percentage score. Percentage scores were assigned as 0, 1, 2, 3, or 4 and intensity scores were assigned 0, 1+, 2+ or 3+. For the analysis of the IHC, a percentage score of 3 or 4 and an intensity score of 2+ or 3+ were categorized as high. Chi-square or Fisher's exact tests were used to compare the high and low groups. In this cohort, 89.7% (26 out of 29) of IBC cases showed high percentages of positive cells staining for the DLX4 protein, while 40.0% (12 out of 30) of normal breast tissue from reduction mammoplasty cases demonstrated DLX4 expression (p < 0.01). In IBC patients, 65.5% of cases showed a high level of staining intensity, compared to 20.0% of normal breast tissues (test, p = 0.001). Intensity to DLX4 was higher in the HER2 negative status (78.3%) than the HER2 positive status (16.7%) (test, p = 0.011). DLX4 expression is higher in the IBC cases in this study of an urban AA population than in normal breast tissue cases. HER2 negative status is positively associated with high intensity of DLX4.
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Affiliation(s)
- Jaehong Jeong
- Department of Oncology, Georgetown University Medical Center, Washington DC 20057, USA
- Comprehensive and Integrative Medicine Institute, Daegu 42473, South Korea
| | - Tammey J. Naab
- Department of Pathology, Howard University Hospital, Washington DC 20059, USA
| | - Aileen I. Fernandez
- Department of Oncology, Georgetown University Medical Center, Washington DC 20057, USA
| | - Martin S. Ongkeko
- Department of Pathology, Georgetown University Medical Center, Washington DC 20057, USA
| | - Kepher H. Makambi
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington DC 20057, USA
| | - Jan K. Blancato
- Department of Oncology, Georgetown University Medical Center, Washington DC 20057, USA
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14
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Lou Y, Fallah Y, Yamane K, Berg PE. BP1, a potential biomarker for breast cancer prognosis. Biomark Med 2018; 12:535-545. [DOI: 10.2217/bmm-2017-0212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Homeobox genes are critical in tumor development. An isoform protein of DLX4 called BP1 is expressed in 80% of invasive ductal breast carcinomas. BP1 overexpression is implicated in an aggressive phenotype and poor prognosis. BP1 upregulation is associated with estrogen receptor negativity so those tumors do not respond to antiestrogens. Breast cancer is the second leading cause of death in women. BP1 could serve as both a novel prognostic biomarker for breast cancer and a therapeutic target. In this review, we address the role of BP1 protein in tumorigenesis of breast cancer and four other malignancies. A number of functions of BP1 in cancer are also discussed.
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Affiliation(s)
- Yaoxian Lou
- Department of Biochemistry & Molecular Medicine, George Washington University, Washington, DC 20037, USA
| | - Yassi Fallah
- Department of Oncology, Georgetown University Medical Center, Lombardi Comprehensive Cancer Center, Washington, DC 20057, USA
| | - Kellie Yamane
- NantOmics, Diagnostic Center in Montgomery County, Rockville, MD 20850, USA
| | - Patricia E Berg
- Department of Biochemistry & Molecular Medicine, George Washington University, Washington, DC 20037, USA
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15
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Sugita B, Gill M, Mahajan A, Duttargi A, Kirolikar S, Almeida R, Regis K, Oluwasanmi OL, Marchi F, Marian C, Makambi K, Kallakury B, Sheahan L, Cavalli IJ, Ribeiro EM, Madhavan S, Boca S, Gusev Y, Cavalli LR. Differentially expressed miRNAs in triple negative breast cancer between African-American and non-Hispanic white women. Oncotarget 2018; 7:79274-79291. [PMID: 27813494 PMCID: PMC5346713 DOI: 10.18632/oncotarget.13024] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/25/2016] [Indexed: 01/09/2023] Open
Abstract
Triple Negative Breast Cancer (TNBC), a clinically aggressive subtype of breast cancer, disproportionately affects African American (AA) women when compared to non-Hispanic Whites (NHW). MiRNAs(miRNAs) play a critical role in these tumors, through the regulation of cancer driver genes. In this study, our goal was to characterize and compare the patterns of miRNA expression in TNBC of AA (n = 27) and NHW women (n = 30). A total of 256 miRNAs were differentially expressed between these groups, and distinct from the ones observed in their respective non-TNBC subtypes. Fifty-five of these miRNAs were mapped in cytobands carrying copy number alterations (CNAs); 26 of them presented expression levels concordant with the observed CNAs. Receiving operating characteristic (ROC) analysis showed a good power (AUC ≥ 0.80; 95% CI) for over 65% of the individual miRNAs and a high combined power with superior sensitivity and specificity (AUC = 0.88 (0.78−0.99); 95% CI) of the 26 miRNA panel in discriminating TNBC between these populations. Subsequent miRNA target analysis revealed their involvement in the interconnected PI3K/AKT, MAPK and insulin signaling pathways. Additionally, three miRNAs of this panel were associated with early age at diagnosis. Altogether, these findings indicated that there are different patterns of miRNA expression between TNBC of AA and NHW women and that their mapping in genomic regions with high levels of CNAs is not merely physical, but biologically relevant to the TNBC phenotype. Once validated in distinct cohorts of AA women, this panel can potentially represent their intrinsic TNBC genome signature.
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Affiliation(s)
- Bruna Sugita
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Mandeep Gill
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Akanskha Mahajan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Anju Duttargi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Saurabh Kirolikar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rodrigo Almeida
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Kenny Regis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Olusayo L Oluwasanmi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Fabio Marchi
- International Research Center-CIPE, A. C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Catalin Marian
- The Ohio State University Comprehensive Cancer Center, Division of Cancer Prevention and Control, College of Medicine, The Ohio State University, Columbus, Ohio.,The University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - Kepher Makambi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Departments of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC USA
| | - Bhaskar Kallakury
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
| | - Laura Sheahan
- Innovation Center for Biomedical Informatics, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Iglenir J Cavalli
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Enilze M Ribeiro
- Department of Genetics, Federal University of Paraná, Curitiba, PR, Brazil
| | - Subha Madhavan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Innovation Center for Biomedical Informatics, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Simina Boca
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Innovation Center for Biomedical Informatics, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Yuriy Gusev
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.,Innovation Center for Biomedical Informatics, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Luciane R Cavalli
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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16
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Mahajan AS, Sugita BM, Duttargi AN, Saenz F, Krawczyk E, McCutcheon JN, Fonseca AS, Kallakury B, Pohlmann P, Gusev Y, Cavalli LR. Genomic comparison of early-passage conditionally reprogrammed breast cancer cells to their corresponding primary tumors. PLoS One 2017; 12:e0186190. [PMID: 29049316 PMCID: PMC5648156 DOI: 10.1371/journal.pone.0186190] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/27/2017] [Indexed: 02/06/2023] Open
Abstract
Conditionally reprogrammed cells (CRCs) are epithelial cells that are directly isolated from patients' specimens and propagated in vitro with feeder cells and a Rho kinase inhibitor. A number of these cells have been generated from biopsies of breast cancer patients, including ductal carcinoma in situ and invasive carcinomas. The characterization of their genomic signatures is essential to determine their ability to reflect the natural biology of their tumors of origin. In this study, we performed the genomic characterization of six newly established invasive breast cancer CRC cultures in comparison to the original patients' primary breast tumors (PBT) from which they derived. The CRCs and corresponding PBTs were simultaneously profiled by genome-wide array-CGH, targeted next generation sequencing and global miRNA expression to determine their molecular similarities in the patterns of copy number alterations (CNAs), gene mutations and miRNA expression levels, respectively. The CRCs' epithelial cells content and ploidy levels were also evaluated by flow cytometry. A similar level of CNAs was observed in the pairs of CRCs/PBTs analyzed by array-CGH, with >95% of overlap for the most frequently affected cytobands. Consistently, targeted next generation sequencing analysis showed the retention of specific somatic variants in the CRCs as present in their original PBTs. Global miRNA profiling closely clustered the CRCs with their PBTs (Pearson Correlation, ANOVA paired test, P<0.05), indicating also similarity at the miRNA expression level; the retention of tumor-specific alterations in a subset of miRNAs in the CRCs was further confirmed by qRT-PCR. These data demonstrated that the human breast cancer CRCs of this study maintained at early passages the overall copy number, gene mutations and miRNA expression patterns of their original tumors. The further characterization of these cells by other molecular and cellular phenotypes at late cell passages, are required to further expand their use as a unique and representative ex-vivo tumor model for basic science and translational breast cancer studies.
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Affiliation(s)
- Akanksha S. Mahajan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Bruna M. Sugita
- Department of Genetics, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Anju N. Duttargi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Francisco Saenz
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Ewa Krawczyk
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Justine N. McCutcheon
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Aline S. Fonseca
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Bhaskar Kallakury
- Department of Pathology, Georgetown University, Washington DC, United States of America
| | - Paula Pohlmann
- Division of Hematology-Oncology, MedStar Georgetown University Hospital, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
| | - Luciane R. Cavalli
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, United States of America
- * E-mail:
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17
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Langa BC, Oliveira MMC, Pereira SRF, Lupicki K, Marian C, Govender D, Panieri E, Hiss D, Cavalli IJ, Abdul-Rasool S, Cavalli LR. Copy Number Analysis of the DLX4 and ERBB2 Genes in South African Breast Cancer Patients. Cytogenet Genome Res 2015; 146:195-203. [PMID: 26524685 DOI: 10.1159/000439155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/19/2022] Open
Abstract
Breast cancer is one of the main causes of cancer death among South African women. Although several risk factors can be attributed to the observed high mortality rate, the biology of the tumors is not extensively investigated. Copy number gain of the DLX4 homeobox gene has been observed in breast cancer in association with poor prognosis and specific racial groups. Therefore, we aimed to assess the copy number and prognostic role of DLX4 in breast cancer from South African patients. Due to the co-location of ERBB2 and DLX4 in the 17q21 region, its copy number was also evaluated. Our results in the analysis of 66 cases demonstrated copy number gains of DLX4 and ERBB2 in 24.1 and 29.7% of the cases, respectively. Linear regression analysis showed no dependency between the copy number alterations in these genes. Although not significant, patients with DLX4 and ERBB2 gains presented a higher frequency of advanced-grade tumors. In addition, copy number alterations of these genes were not significantly differently observed in the 3 main racial groups of the Western Cape population: Colored, White, and Black. These findings indicate that gains of DLX4 and ERBB2 occur in South African breast cancer patients irrespectively of their race and factors known to influence prognosis.
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