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Dominguez-Ortiz J, Álvarez-Gómez RM, Montiel-Manríquez R, Cedro-Tanda A, Alcaraz N, Castro-Hernández C, Bautista-Hinojosa L, Contreras-Espinosa L, Torres-Maldonado L, Fragoso-Ontiveros V, Sánchez-Contreras Y, González-Barrios R, la Fuente-Hernández MAD, Mejía-Aguayo MDLL, Juárez-Figueroa U, Padua-Bracho A, Sosa-León R, Obregon-Serrano G, Vidal-Millán S, Núñez-Martínez PM, Pedroza-Torres A, Nicasio-Arzeta S, Rodríguez A, Luna F, Cisneros-Soberanis F, Frías S, Arriaga-Canon C, Herrera-Montalvo LA. A Molecular Characterization of the Allelic Expression of the BRCA1 Founder Δ9-12 Pathogenic Variant and Its Potential Clinical Relevance in Hereditary Cancer. Int J Mol Sci 2024; 25:6773. [PMID: 38928478 PMCID: PMC11204022 DOI: 10.3390/ijms25126773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Hereditary breast and ovarian cancer (HBOC) syndrome is a genetic condition that increases the risk of breast cancer by 80% and that of ovarian cancer by 40%. The most common pathogenic variants (PVs) causing HBOC occur in the BRCA1 gene, with more than 3850 reported mutations in the gene sequence. The prevalence of specific PVs in BRCA1 has increased across populations due to the effect of founder mutations. Therefore, when a founder mutation is identified, it becomes key to improving cancer risk characterization and effective screening protocols. The only founder mutation described in the Mexican population is the deletion of exons 9 to 12 of BRCA1 (BRCA1Δ9-12), and its description focuses on the gene sequence, but no transcription profiles have been generated for individuals who carry this gene. In this study, we describe the transcription profiles of cancer patients and healthy individuals who were heterozygous for PV BRCA1Δ9-12 by analyzing the differential expression of both alleles compared with the homozygous BRCA1 control group using RT-qPCR, and we describe the isoforms produced by the BRCA1 wild-type and BRCA1Δ9-12 alleles using nanopore long-sequencing. Using the Kruskal-Wallis test, our results showed a similar transcript expression of the wild-type allele between the healthy heterozygous group and the homozygous BRCA1 control group. An association between the recurrence and increased expression of both alleles in HBOC patients was also observed. An analysis of the sequences indicated four wild-type isoforms with diagnostic potential for discerning individuals who carry the PV BRCA1Δ9-12 and identifying which of them has developed cancer.
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Affiliation(s)
- Julieta Dominguez-Ortiz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
- Instituto Nacional de Cancerología, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Mexico City 04510, Mexico
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rosa M. Álvarez-Gómez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Alberto Cedro-Tanda
- Núcleo B de Innovación en Medicina de Precisión, Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico;
| | - Nicolás Alcaraz
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, 2200 Copenhagen, Denmark;
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Luis Bautista-Hinojosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Leda Torres-Maldonado
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
| | - Verónica Fragoso-Ontiveros
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Yuliana Sánchez-Contreras
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Marcela Angélica De la Fuente-Hernández
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - María de la Luz Mejía-Aguayo
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Ulises Juárez-Figueroa
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
| | - Alejandra Padua-Bracho
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rodrigo Sosa-León
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Gabriela Obregon-Serrano
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Silvia Vidal-Millán
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Paulina María Núñez-Martínez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Abraham Pedroza-Torres
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Sergio Nicasio-Arzeta
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80521, USA;
| | - Alfredo Rodríguez
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México City 04510, Mexico
| | - Fernando Luna
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King’s Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK;
| | - Sara Frías
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México City 04510, Mexico
| | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico
| | - Luis A. Herrera-Montalvo
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico
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Kim DM, Feilotter HE, Davey SK. BRCA1 Variant Assessment Using a Simple Analytic Assay. J Appl Lab Med 2022; 7:674-688. [PMID: 35021209 DOI: 10.1093/jalm/jfab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND We previously developed a biological assay to accurately predict BRCA1 (BRCA1 DNA repair associated) mutation status, based on gene expression profiles of Epstein-Barr virus-transformed lymphoblastoid cell lines. The original work was done using whole genome expression microarrays, and nearest shrunken centroids analysis. While these approaches are appropriate for model building, they are difficult to implement clinically, where more targeted testing and analysis are required for time and cost savings. METHODS Here, we describe adaptation of the original predictor to use the NanoString nCounter platform for testing, with analysis based on the k-top scoring pairs (k-TSP) method. RESULTS Assessing gene expression using the nCounter platform on a set of lymphoblastoid cell lines yielded 93.8% agreement with the microarray-derived data, and 87.5% overall correct classification of BRCA1 carriers and controls. Using the original gene expression microarray data used to develop our predictor with nearest shrunken centroids, we rebuilt a classifier based on the k-TSP method. This classifier relies on the relative expression of 10 pairs of genes, compared to the original 43 identified by nearest shrunken centroids (NSC), and was 96.2% concordant with the original training set prediction, with a 94.3% overall correct classification of BRCA1 carriers and controls. CONCLUSIONS The k-TSP classifier was shown to accurately predict BRCA1 status using data generated on the nCounter platform and is feasible for initiating a clinical validation.
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Affiliation(s)
- Daniel M Kim
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Scott K Davey
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Departments of Oncology and Biomedical and Molecular Sciences, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
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Genome-Wide Gene Expression Analyses of BRCA1- and BRCA2-Associated Breast and Ovarian Tumours. Cancers (Basel) 2020; 12:cancers12103015. [PMID: 33081408 PMCID: PMC7603076 DOI: 10.3390/cancers12103015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 increase cumulative lifetime risk up to 75% for breast cancer and 76% for ovarian cancer. Genetic testing for BRCA1 and BRCA2 pathogenic variants has become an important part of clinical practice for cancer risk assessment and for reducing individual risk of developing cancer. Genetic testing can produce three outcomes: positive (a pathogenic variant), uninformative (no pathogenic variant) and uncertain significance (a variant of unknown clinical significance). More than one third of BRCA1 and BRCA2 variants identified have been classified as variants of uncertain significance, presenting a challenge for clinicians. To address this important clinical challenge, a number of studies have been undertaken to establish a gene expression phenotype for pathogenic BRCA1 and BRCA2 variant carriers in several diseased and normal tissues. However, the consistency of gene expression phenotypes described in studies has been poor. To determine if gene expression analysis has been a successful approach for variant classification, we describe the design and comparability of 23 published gene expression studies that have profiled cells from BRCA1 and BRCA2 pathogenic variant carriers. We show the impact of advancements in expression-based technologies, the importance of developing larger study cohorts and the necessity to better understand variables affecting gene expression profiles across different tissue types.
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Zahavi T, Sonnenblick A, Shimshon Y, Kadouri L, Peretz T, Salmon AY, Salmon-Divon M. SYK expression level distinguishes control from BRCA1-mutated lymphocytes. Cancer Manag Res 2018; 10:589-598. [PMID: 29618939 PMCID: PMC5875411 DOI: 10.2147/cmar.s156359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background About 5%-10% of breast cancer and 10%-15% of ovarian cancer are hereditary. BRCA1 and BRCA2 are the most common germline mutations found in both inherited breast and ovarian cancers. Once these mutations are identified and classified, a course of action to reduce the risk of developing either ovarian or breast cancer - including surveillance and surgery - is carried out. Purpose The purpose of the current research is to characterize the gene expression differences between healthy cells harboring a mutation in BRCA1/2 genes and normal cells. This will allow detection of candidate genes and help identify women who carry functional BRCA1/2 mutations, which cannot always be detected by the available sequencing methods, for example, carriers of mutations found in regulatory sequences of the genes. Materials and methods Our cohort consisted of 50 healthy women, of whom 24 were individuals with BRCA1 or BRCA2 heterozygous mutations and 26 were non-carrier controls. RNA purified from non-irradiated lymphocytes of nine BRCA1/2 mutation carriers versus four control mutation-negative individuals was utilized for RNA-Seq analysis. The selected RNA-Seq transcripts were validated, and the levels of spleen tyrosine kinase (SYK) mRNA were measured by using real-time quantitative polymerase chain reaction. Results Differences in gene expression were found when comparing untreated lymphocytes of BRCA1/2 mutation carriers and controls. Among others, the SYK gene was identified as being differently expressed for BRCA1/2 mutation carriers. The expression level of SYK was significantly higher in untreated healthy lymphocytes of BRCA1 heterozygote carriers compared with controls, regardless of irradiation. In contrast to normal tissues, in cancerous breast tissues, the expression levels of the BRCA1 and SYK genes were not intercorrelated. Conclusion Collectively, our observations demonstrate that SYK may prove to be a good candidate for better diagnosis, treatment, and prevention of BRCA1 mutation-associated breast cancer.
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Affiliation(s)
- Tamar Zahavi
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel.,Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Amir Sonnenblick
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel.,Sackler Faculty of Medicine, Sourasky Medical Center, Institute of Oncology, Tel Aviv University, Tel Aviv, Israel
| | - Yael Shimshon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Luna Kadouri
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Asher Y Salmon
- Sharett Institute of Oncology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
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El Khachibi M, El Karroumi M, Ayoubi SE, El Kadmiri N, Nadifi S. Assessment of the expression of the BRCA1, BRCA2, TP53, MDM2, BAX and CASP-3 genes in normal and tumor tissues for patients with breast cancer in Morocco. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2017.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Transcriptional signature of lymphoblastoid cell lines of BRCA1, BRCA2 and non- BRCA1/2 high risk breast cancer families. Oncotarget 2017; 8:78691-78712. [PMID: 29108258 PMCID: PMC5667991 DOI: 10.18632/oncotarget.20219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
Approximately 25% of hereditary breast cancer cases are associated with a strong familial history which can be explained by mutations in BRCA1 or BRCA2 and other lower penetrance genes. The remaining high-risk families could be classified as BRCAX (non-BRCA1/2) families. Gene expression involving alternative splicing represents a well-known mechanism regulating the expression of multiple transcripts, which could be involved in cancer development. Thus using RNA-seq methodology, the analysis of transcriptome was undertaken to potentially reveal transcripts implicated in breast cancer susceptibility and development. RNA was extracted from immortalized lymphoblastoid cell lines of 117 women (affected and unaffected) coming from BRCA1, BRCA2 and BRCAX families. Anova analysis revealed a total of 95 transcripts corresponding to 85 different genes differentially expressed (Bonferroni corrected p-value <0.01) between those groups. Hierarchical clustering allowed distinctive subgrouping of BRCA1/2 subgroups from BRCAX individuals. We found 67 transcripts, which could discriminate BRCAX from BRCA1/BRCA2 individuals while 28 transcripts discriminate affected from unaffected BRCAX individuals. To our knowledge, this represents the first study identifying transcripts differentially expressed in lymphoblastoid cell lines from major classes of mutation-related breast cancer subgroups, namely BRCA1, BRCA2 and BRCAX. Moreover, some transcripts could discriminate affected from unaffected BRCAX individuals, which could represent potential therapeutic targets for breast cancer treatment.
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Kusaka M, Okamoto M, Takenaka M, Sasaki H, Fukami N, Kataoka K, Ito T, Kenmochi T, Hoshinaga K, Shiroki R. Gene Expression Profiling of Peripheral Blood From Kidney Transplant Recipients for the Early Detection of Digestive System Cancer. Transplant Proc 2017; 49:1056-1060. [PMID: 28583526 DOI: 10.1016/j.transproceed.2017.03.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Kidney transplant recipients are at increased risk of developing cancer in comparison with the general population. To effectively manage post-transplantation malignancies, it is essential to proactively monitor patients. A long-term intensive screening program was associated with a reduced incidence of cancer after transplantation. This study evaluated the usefulness of the gene expression profiling of peripheral blood samples obtained from kidney transplant patients and adopted a screening test for detecting cancer of the digestive system (gastric, colon, pancreas, and biliary tract). STUDY DESIGN AND METHOD Nineteen patients were included in this study and a total of 53 gene expression screening tests were performed. The gene expression profiles of blood-delivered total RNA and whole genome human gene expression profiles were obtained. We investigated the expression levels of 2665 genes associated with digestive cancers and counted the number of genes in which expression was altered. A hierarchical clustering analysis was also performed. The final prediction of the cancer possibility was determined according to an algorithm. RESULTS The number of genes in which expression was altered was significantly increased in the kidney transplant recipients in comparison with the general population (1091 ± 63 vs 823 ± 94; P = .0024). The number of genes with altered expression decreased after the induction of mechanistic target of rapamycin (mTOR) inhibitor (1484 ± 227 vs 883 ± 154; P = .0439). No cases of possible digestive cancer were detected in this study period. CONCLUSION The gene expression profiling of peripheral blood samples may be a useful and noninvasive diagnostic tool that allows for the early detection of cancer of the digestive system.
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Affiliation(s)
- M Kusaka
- Department of Urology, Fujita-Health University School of Medicine, Toyoake, Aichi, Japan.
| | | | - M Takenaka
- Department of Urology, Fujita-Health University School of Medicine, Toyoake, Aichi, Japan
| | - H Sasaki
- Department of Urology, Fujita-Health University School of Medicine, Toyoake, Aichi, Japan
| | - N Fukami
- Department of Urology, Fujita-Health University School of Medicine, Toyoake, Aichi, Japan
| | | | - T Ito
- Department of Organ Transplant Surgery, Fujita-Health University, Toyoake, Aichi, Japan
| | - T Kenmochi
- Department of Organ Transplant Surgery, Fujita-Health University, Toyoake, Aichi, Japan
| | - K Hoshinaga
- Department of Urology, Fujita-Health University School of Medicine, Toyoake, Aichi, Japan
| | - R Shiroki
- Department of Urology, Fujita-Health University School of Medicine, Toyoake, Aichi, Japan
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Etzold A, Galetzka D, Weis E, Bartsch O, Haaf T, Spix C, Itzel T, Schweiger S, Strand D, Strand S, Zechner U. CAF-like state in primary skin fibroblasts with constitutional BRCA1 epimutation sheds new light on tumor suppressor deficiency-related changes in healthy tissue. Epigenetics 2016; 11:120-31. [PMID: 26949839 DOI: 10.1080/15592294.2016.1140295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Constitutive epimutations of tumor suppressor genes are increasingly considered as cancer predisposing factors equally to sequence mutations. In light of the emerging role of the microenvironment for cancer predisposition, initiation, and progression, we aimed to characterize the consequences of a BRCA1 epimutation in cells of mesenchymal origin. We performed a comprehensive molecular and cellular comparison of primary dermal fibroblasts taken from a monozygous twin pair discordant for recurrent cancers and BRCA1 epimutation, whose exceptional clinical case we previously reported in this journal. Comparative transcriptome analysis identified differential expression of extracellular matrix-related genes and pro-tumorigenic growth factors, such as collagens and CXC chemokines. Moreover, genes known to be key markers of so called cancer-associated fibroblasts (CAFs), such as ACTA2, FAP, PDPN, and TNC, were upregulated in fibroblasts of the affected twin (BRCA1(mosMe)) in comparison to those of the healthy twin (BRCA1(wt)). Further analyses detected CAF-typical cellular features, including an elevated growth rate, enhanced migration, altered actin architecture and increased production of ketone bodies in BRCA1(mosMe) fibroblasts compared to BRCA1(wt) fibroblasts. In addition, conditioned medium of BRCA1(mosMe) fibroblasts was more potent than conditioned medium of BRCA1(wt) fibroblasts to promote cell proliferation in an epithelial and a cancer cell line. Our data demonstrate, that a CAF-like state is not an exclusive feature of tumor-associated tissue but also exists in healthy tissue with tumor suppressor deficiency. The naturally occurring phenomenon of twin fibroblasts differing in their BRCA1 methylation status revealed to be a unique powerful tool for exploring tumor suppressor deficiency-related changes in healthy tissue, reinforcing their significance for cancer predisposition.
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Affiliation(s)
- Anna Etzold
- a Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Danuta Galetzka
- a Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Eva Weis
- a Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Oliver Bartsch
- a Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Thomas Haaf
- b Institute of Human Genetics, Julius Maximilians University , Würzburg , Germany
| | - Claudia Spix
- c Institute of Medical Biometry, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Timo Itzel
- c Institute of Medical Biometry, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Susann Schweiger
- a Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Dennis Strand
- d First Department of Internal Medicine , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Susanne Strand
- d First Department of Internal Medicine , University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
| | - Ulrich Zechner
- a Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz , Germany
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Vuillaume ML, Kwiatkowski F, Uhrhammer N, Bidet Y, Bignon YJ. [Analysis of gene expression data regulated by clock-genes: methodological approach and optimization]. PATHOLOGIE-BIOLOGIE 2013; 61:e89-e95. [PMID: 23122513 DOI: 10.1016/j.patbio.2010.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND In microarray data, wide-scale correlations are numerous and increase the number of genes correlated to a test condition (phenotype, mutation status, etc.) either positively or negatively. Several methods have been developed to limit the effect of such correlations on the false discovery rate, but these may reject too many genes that have a mild or indirect impact on the studied condition. We propose here a simple methodology to correct this spurious effect without eliminating weak but true correlations. RESULTS This methodology was applied to a microarray dataset designed to distinguish heterozygous BRCA1 mutation carriers from non-carriers. As our samples were collected at different times in the morning, we evaluated the effect of correlations due to circadian rhythm. The circadian system is a well-known correlation network, regulated by a small number of period genes whose expression varies throughout the day in predictable ways. The downstream effects of this variation on the expression of other genes, however, are incompletely characterized. We used two different strategies to correct this correlation bias, by either dividing or multiplying the expression of correlated genes by the expression of the considered period gene according to the sign of the correlation between the period gene and correlated gene (respectively positive or negative). CONCLUSIONS We observed a linear relationship between the number of false-positive/negative genes and the strength of the correlation of the candidate gene to the test condition. BRCA1 was highly correlated to the period gene Per1; our correction methodology enabled us to recover genes coding for BRCA1-interacting proteins which were not selected in the initial direct analysis. This methodology may be valuable for other studies and can be applied very easily in case of well-known correlation networks.
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Affiliation(s)
- M-L Vuillaume
- Laboratoire d'oncologie moléculaire, centre Jean-Perrin, 58, rue Montalembert, 63011 Clermont-Ferrand, France.
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Gene expression profile of peripheral blood lymphocytes from renal cell carcinoma patients treated with IL-2, interferon-α and dendritic cell vaccine. PLoS One 2012; 7:e50221. [PMID: 23226513 PMCID: PMC3513309 DOI: 10.1371/journal.pone.0050221] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 10/22/2012] [Indexed: 12/03/2022] Open
Abstract
Lymphocytes are a key component of the immune system and their differentiation and function are directly influenced by cancer. We examined peripheral blood lymphocyte (PBL) gene expression as a biomarker of illness and treatment effect using the Affymetrix Human Gene ST1 platform in patients with metastatic renal cell carcinoma (mRCC) who received combined treatment with IL-2, interferon-?-2a and dendritic cell vaccine. We examined gene expression, cytokine levels in patient serum and lymphocyte subsets as determined by flow cytometry (FCM). Pre-treatment PBLs from patients with mRCC exhibit a gene expression profile and serum cytokine profile consistent with inflammation and proliferation not found in healthy donors (HD). PBL gene expression from patients with mRCC showed increased mRNA of genes involved with T-cell and TREG-cell activation pathways, which was also reflected in lymphocyte subset distribution. Overall, PBL gene expression post-treatment (POST) was not significantly different than pre-treatment (PRE). Nevertheless, treatment related changes in gene expression (post-treatment minus pre-treatment) revealed an increased expression of T-cell and B-cell receptor signaling pathways in responding (R) patients compared to non-responding (NR) patients. In addition, we observed down-regulation of TREG-cell pathways post-treatment in R vs. NR patients. While exploratory in nature, this study supports the hypothesis that enhanced inflammatory cytotoxic pathways coupled with blunting of the regulatory pathways is necessary for effective anti-cancer activity associated with immune therapy. This type of analysis can potentially identify additional immune therapeutic targets in patients with mRCC.
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Gertz EM, Sengupta K, Difilippantonio MJ, Ried T, Schäffer AA. Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted. BMC Genomics 2009; 10:566. [PMID: 19948035 PMCID: PMC2791105 DOI: 10.1186/1471-2164-10-566] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 11/30/2009] [Indexed: 12/31/2022] Open
Abstract
Background While attempting to reanalyze published data from Agilent 4 × 44 human expression chips, we found that some of the 60-mer olignucleotide features could not be interpreted as representing single human genes. For example, some of the oligonucleotides align with the transcripts of more than one gene. We decided to check the annotations for all autosomes and the X chromosome systematically using bioinformatics methods. Results Out of 42683 reporters, we found that 25505 (60%) passed all our tests and are considered "fully valid". 9964 (23%) reporters did not have a meaningful identifier, mapped to the wrong chromosome, or did not pass basic alignment tests preventing us from correlating the expression values of these reporters with a unique annotated human gene. The remaining 7214 (17%) reporters could be associated with either a unique gene or a unique intergenic location, but could not be mapped to a transcript in RefSeq. The 7214 reporters are further partitioned into three different levels of validity. Conclusion Expression array studies should evaluate the annotations of reporters and remove those reporters that have suspect annotations. This evaluation can be done systematically and semi-automatically, but one must recognize that data sources are frequently updated leading to slightly changing validation results over time.
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Affiliation(s)
- E Michael Gertz
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
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