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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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Elshwekh H, Alhudiri IM, Elzagheid A, Enattah N, Abbassi Y, Abou Assali L, Marino I, Stuani C, Buratti E, Romano M. Assessing the Impact of Novel BRCA1 Exon 11 Variants on Pre-mRNA Splicing. Cells 2024; 13:824. [PMID: 38786046 PMCID: PMC11119505 DOI: 10.3390/cells13100824] [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: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Our study focused on assessing the effects of three newly identified BRCA1 exon 11 variants (c.1019T>C, c.2363T>G, and c.3192T>C) on breast cancer susceptibility. Using computational predictions and experimental splicing assays, we evaluated their potential as pathogenic mutations. Our in silico analyses suggested that the c.2363T>G and c.3192T>C variants could impact both splicing and protein function, resulting in the V340A and V788G mutations, respectively. We further examined their splicing effects using minigene assays in MCF7 and SKBR3 breast cancer cell lines. Interestingly, we found that the c.2363T>G variant significantly altered splicing patterns in MCF7 cells but not in SKBR3 cells. This finding suggests a potential influence of cellular context on the variant's effects. While attempts to correlate in silico predictions with RNA binding factors were inconclusive, this observation underscores the complexity of splicing regulation. Splicing is governed by various factors, including cellular contexts and protein interactions, making it challenging to predict outcomes accurately. Further research is needed to fully understand the functional consequences of the c.2363T>G variant in breast cancer pathogenesis. Integrating computational predictions with experimental data will provide valuable insights into the role of alternative splicing regulation in different breast cancer types and stages.
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Affiliation(s)
- Halla Elshwekh
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Inas M. Alhudiri
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Adam Elzagheid
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Nabil Enattah
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Yasmine Abbassi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Lubna Abou Assali
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Ilenia Marino
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio, 28, 34127 Trieste, Italy
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Aretini P, Presciuttini S, Pastore A, Galli A, Panepinto S, Tancredi M, Ghilli M, Guglielmi C, Sidoti D, Congregati C, Caligo MA. The BRCA1 c.4096+1G>A Is a Founder Variant Which Originated in Ancient Times. Int J Mol Sci 2023; 24:15507. [PMID: 37958491 PMCID: PMC10648645 DOI: 10.3390/ijms242115507] [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: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Approximately 30-50% of hereditary breast and ovarian cancer (HBOC) is due to the presence of germline pathogenic variants in the BRCA1 (OMIM 113705) and BRCA2 (OMIM 600185) onco-suppressor genes, which are involved in DNA damage response. Women who carry pathogenic BRCA1 variants are particularly likely to develop breast cancer (BC) and ovarian cancer (OC), with a 45-79 percent and 39-48 percent chance, respectively. The BRCA1 c.4096+1G>A variant has been frequently ascertained in Tuscany, Italy, and it has also been detected in other Italian regions and other countries. Its pathogenetic status has been repeatedly changed from a variant of uncertain significance, to pathogenic, to likely pathogenic. In our study, 48 subjects (38 of whom are carriers) from 27 families were genotyped with the Illumina OncoArray Infinium platform (533,531 SNPs); a 20 Mb region (24.6 cM) around BRCA1, including 4130 SNPs (21 inside BRCA1) was selected for haplotype analysis. We used a phylogenetic method to estimate the time to the most recent common ancestor (MRCA) of BRCA1 c.4096+1G>A founder pathogenic variant. This analysis suggests that the MRCA lived about 155 generations ago-around 3000 years ago.
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Affiliation(s)
- Paolo Aretini
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy;
| | - Silvano Presciuttini
- Dipartimento di Ricerca Traslazionale e Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 56126 Pisa, Italy;
| | - Aldo Pastore
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy;
- Laboratorio NEST, Scuola Normale Superiore, 56126 Pisa, Italy
| | - Alvaro Galli
- Istituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche (CNR), 56124 Pisa, Italy;
| | - Sara Panepinto
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Mariella Tancredi
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Matteo Ghilli
- Breast Unit, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Chiara Guglielmi
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Diletta Sidoti
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
| | - Caterina Congregati
- Genetica Medica, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Maria Adelaide Caligo
- Laboratorio di Genetica Molecolare, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy; (S.P.); (M.T.); (C.G.); (D.S.)
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Pettitt SJ, Shao N, Zatreanu D, Frankum J, Bajrami I, Brough R, Krastev DB, Roumeliotis TI, Choudhary JS, Lorenz S, Rust A, de Bono JS, Yap TA, Tutt ANJ, Lord CJ. A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant. Oncogene 2023; 42:2701-2709. [PMID: 37491606 PMCID: PMC10473960 DOI: 10.1038/s41388-023-02782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Although PARP inhibitors (PARPi) now form part of the standard-of-care for the treatment of homologous recombination defective cancers, de novo and acquired resistance limits their overall effectiveness. Previously, overexpression of the BRCA1-∆11q splice variant has been shown to cause PARPi resistance. How cancer cells achieve increased BRCA1-∆11q expression has remained unclear. Using isogenic cells with different BRCA1 mutations, we show that reduction in HUWE1 leads to increased levels of BRCA1-∆11q and PARPi resistance. This effect is specific to cells able to express BRCA1-∆11q (e.g. BRCA1 exon 11 mutant cells) and is not seen in BRCA1 mutants that cannot express BRCA1-∆11q, nor in BRCA2 mutant cells. As well as increasing levels of BRCA1-∆11q protein in exon 11 mutant cells, HUWE1 silencing also restores RAD51 nuclear foci and platinum salt resistance. HUWE1 catalytic domain mutations were also seen in a case of PARPi resistant, BRCA1 exon 11 mutant, high grade serous ovarian cancer. These results suggest how elevated levels of BRCA1-∆11q and PARPi resistance can be achieved, identify HUWE1 as a candidate biomarker of PARPi resistance for assessment in future clinical trials and illustrate how some PARPi resistance mechanisms may only operate in patients with particular BRCA1 mutations.
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Affiliation(s)
- Stephen J Pettitt
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Nan Shao
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Diana Zatreanu
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Dragomir B Krastev
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | | | | | - Sonja Lorenz
- Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Alistair Rust
- The Institute of Cancer Research, London, SW3 6JB, UK
| | - Johann S de Bono
- The Institute of Cancer Research, The Royal Marsden Hospital, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Timothy A Yap
- The Institute of Cancer Research, The Royal Marsden Hospital, Downs Road, Sutton, Surrey, SM2 5PT, UK
- University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, Houston, TX, 77030, USA
| | - Andrew N J Tutt
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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5
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Nesic K, Krais JJ, Vandenberg CJ, Wang Y, Patel P, Cai KQ, Kwan T, Lieschke E, Ho GY, Barker HE, Bedo J, Casadei S, Farrell A, Radke M, Shield-Artin K, Penington JS, Geissler F, Kyran E, Zhang F, Dobrovic A, Olesen I, Kristeleit R, Oza A, Ratnayake G, Traficante N, DeFazio A, Bowtell DDL, Harding TC, Lin K, Swisher EM, Kondrashova O, Scott CL, Johnson N, Wakefield MJ. BRCA1 secondary splice-site mutations drive exon-skipping and PARP inhibitor resistance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.20.23287465. [PMID: 36993400 PMCID: PMC10055590 DOI: 10.1101/2023.03.20.23287465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
BRCA1 splice isoforms Δ11 and Δ11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out the mutation-containing exon, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers of BRCA1 exon skipping remain undetermined. We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with BRCA1 exon 11 frameshift mutations for exon skipping and therapy response, including a matched PDX pair derived from a patient pre- and post-chemotherapy/PARPi. BRCA1 exon 11 skipping was elevated in PARPi resistant PDX tumors. Two independent PDX models acquired secondary BRCA1 splice site mutations (SSMs), predicted in silico to drive exon skipping. Predictions were confirmed using qRT-PCR, RNA sequencing, western blots and BRCA1 minigene modelling. SSMs were also enriched in post-PARPi ovarian cancer patient cohorts from the ARIEL2 and ARIEL4 clinical trials. We demonstrate that SSMs drive BRCA1 exon 11 skipping and PARPi resistance, and should be clinically monitored, along with frame-restoring secondary mutations.
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Affiliation(s)
- Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | | | | | - Tanya Kwan
- Clovis Oncology Inc., San Francisco, CA, USA
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gwo-Yaw Ho
- School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Bedo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | - Andrew Farrell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Marc Radke
- University of Washington, Seattle, WA, USA
| | - Kristy Shield-Artin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jocelyn S. Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Franziska Geissler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Elizabeth Kyran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Fan Zhang
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, Victoria, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, Victoria, Australia
| | - Inger Olesen
- The Andrew Love Cancer Centre, Barwon Health, Geelong, Victoria, Australia
| | - Rebecca Kristeleit
- Department of Oncology, Guys and St Thomas’ NHS Foundation Trust, London, UK
- National Institute for Health Research, University College London Hospitals Clinical Research Facility, London, UK
| | - Amit Oza
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | - Nadia Traficante
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | | | - Anna DeFazio
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council New South Wales, Sydney, New South Wales, Australia
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynecological Oncology, Westmead Hospital, Western Sydney Local Health District, New South Wales, Australia
| | - David D. L. Bowtell
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | | | - Kevin Lin
- Clovis Oncology Inc., San Francisco, CA, USA
| | | | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, VIC, Australia
| | | | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, VIC, Australia
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6
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Su T, Hollas MAR, Fellers RT, Kelleher NL. Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics. Annu Rev Biomed Data Sci 2023; 6:357-376. [PMID: 37561601 PMCID: PMC10840079 DOI: 10.1146/annurev-biodatasci-020722-044021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Alternative splicing is pivotal to the regulation of gene expression and protein diversity in eukaryotic cells. The detection of alternative splicing events requires specific omics technologies. Although short-read RNA sequencing has successfully supported a plethora of investigations on alternative splicing, the emerging technologies of long-read RNA sequencing and top-down mass spectrometry open new opportunities to identify alternative splicing and protein isoforms with less ambiguity. Here, we summarize improvements in short-read RNA sequencing for alternative splicing analysis, including percent splicing index estimation and differential analysis. We also review the computational methods used in top-down proteomics analysis regarding proteoform identification, including the construction of databases of protein isoforms and statistical analyses of search results. While many improvements in sequencing and computational methods will result from emerging technologies, there should be future endeavors to increase the effectiveness, integration, and proteome coverage of alternative splicing events.
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Affiliation(s)
- Taojunfeng Su
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA;
| | - Michael A R Hollas
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA;
- Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
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7
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Targeting Homologous Recombination Deficiency in Ovarian Cancer with PARP Inhibitors: Synthetic Lethal Strategies That Impact Overall Survival. Cancers (Basel) 2022; 14:cancers14194621. [PMID: 36230543 PMCID: PMC9563432 DOI: 10.3390/cancers14194621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Synthetic lethality approaches to cancer therapy involves combining events to cause cancer cell death. Using this strategy, major advances have occurred in the treatment of women with ovarian cancer who have defects in the Homologous Recombination Repair (HRR) pathway. When the HRR pathway is defective, due to mutations or epigenetic changes in genes such as BRCA1 or BRCA2, cells can no longer accurately repair double strand breaks (DSBs). Capitalising on this weakness, pharmacological inhibition of poly (ADP-ribose) polymerase (PARP) that function to repair single strand breaks (SSBs) leads to synthetic lethality in cells with defective HRR. PARP inhibitors (PARPis) including olaparib, niraparib and rucaparib are approved for the clinical management of women with ovarian cancer. Understanding and overcoming issues of acquired resistance to PARPis, extending these strategies to benefit more patients and combining PARPis with other drugs, including immunotherapies, are of high priority in the field today. Abstract The advent of molecular targeted therapies has made a significant impact on survival of women with ovarian cancer who have defects in homologous recombination repair (HRR). High-grade serous ovarian cancer (HGSOC) is the most common histological subtype of ovarian cancer, with over 50% displaying defective HRR. Poly ADP ribose polymerases (PARPs) are a family of enzymes that catalyse the transfer of ADP-ribose to target proteins, functioning in fundamental cellular processes including transcription, chromatin remodelling and DNA repair. In cells with deficient HRR, PARP inhibitors (PARPis) cause synthetic lethality leading to cell death. Despite the major advances that PARPis have heralded for women with ovarian cancer, questions and challenges remain, including: can the benefits of PARPis be brought to a wider range of women with ovarian cancer; can other drugs in clinical use function in a similar way or with greater efficacy than currently clinically approved PARPis; what can we learn from long-term responders to PARPis; can PARPis sensitise ovarian cancer cells to immunotherapy; and can synthetic lethal strategies be employed more broadly to develop new therapies for women with ovarian cancer. We examine these, and other, questions with focus on improving outcomes for women with ovarian cancer.
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8
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Ruiz de Garibay G, Fernandez-Garcia I, Mazoyer S, Leme de Calais F, Ameri P, Vijayakumar S, Martinez-Ruiz H, Damiola F, Barjhoux L, Thomassen M, Andersen LVB, Herranz C, Mateo F, Palomero L, Espín R, Gómez A, García N, Jimenez D, Bonifaci N, Extremera AI, Castaño J, Raya A, Eyras E, Puente XS, Brunet J, Lázaro C, Radice P, Barnes DR, Antoniou AC, Spurdle AB, de la Hoya M, Baralle D, Barcellos-Hoff MH, Pujana MA. Altered regulation of BRCA1 exon 11 splicing is associated with breast cancer risk in carriers of BRCA1 pathogenic variants. Hum Mutat 2021; 42:1488-1502. [PMID: 34420246 DOI: 10.1002/humu.24276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 11/12/2022]
Abstract
Germline pathogenic variants in BRCA1 confer a high risk of developing breast and ovarian cancer. The BRCA1 exon 11 (formally exon 10) is one of the largest exons and codes for the nuclear localization signals of the corresponding gene product. This exon can be partially or entirely skipped during pre-mRNA splicing, leading to three major in-frame isoforms that are detectable in most cell types and tissue, and in normal and cancer settings. However, it is unclear whether the splicing imbalance of this exon is associated with cancer risk. Here we identify a common genetic variant in intron 10, rs5820483 (NC_000017.11:g.43095106_43095108dup), which is associated with exon 11 isoform expression and alternative splicing, and with the risk of breast cancer, but not ovarian cancer, in BRCA1 pathogenic variant carriers. The identification of this genetic effect was confirmed by analogous observations in mouse cells and tissue in which a loxP sequence was inserted in the syntenic intronic region. The prediction that the rs5820483 minor allele variant would create a binding site for the splicing silencer hnRNP A1 was confirmed by pull-down assays. Our data suggest that perturbation of BRCA1 exon 11 splicing modifies the breast cancer risk conferred by pathogenic variants of this gene.
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Affiliation(s)
- Gorka Ruiz de Garibay
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Ignacio Fernandez-Garcia
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, USA
| | - Sylvie Mazoyer
- Equipe GENDEV, INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, Université Lyon 1, Université St Etienne, Lyon, France
| | - Flavia Leme de Calais
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Pietro Ameri
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, USA
| | - Sangeetha Vijayakumar
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, USA
| | - Haydeliz Martinez-Ruiz
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, USA
| | - Francesca Damiola
- Department of Biopathology, Pathology Research Platform, Centre Léon Bérard, Lyon, France
| | - Laure Barjhoux
- Department of Biopathology, Pathology Research Platform, Centre Léon Bérard, Lyon, France
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Lars V B Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Carmen Herranz
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Francesca Mateo
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Luis Palomero
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Roderic Espín
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Antonio Gómez
- Gene Regulation, Stem Cells and Cancer, Center for Genomic Regulation (CRG), Barcelona, Catalonia, Spain
| | - Nadia García
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Daniel Jimenez
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Núria Bonifaci
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Ana I Extremera
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Julio Castaño
- Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Angel Raya
- Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), L'Hospitalet del Llobregat, Barcelona, Spain.,Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Eduardo Eyras
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain.,Department of Genome Sciences, The John Curtin School of Medical Research, EMBL Australia Partner Laboratory Network, Australian National University, Canberra, Australia
| | - Xose S Puente
- Department of Biochemistry and Molecular Biology, University Institute of Oncology, University of Oviedo, Oviedo, Spain.,Biomedical Research Centre in Cancer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, and Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
| | - Conxi Lázaro
- Biomedical Research Centre in Cancer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, and Girona Biomedical Research Institute (IDIBGI), Girona, Catalonia, Spain
| | -
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
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- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniel R Barnes
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Amanda B Spurdle
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Miguel de la Hoya
- Biomedical Research Centre in Cancer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain.,Molecular Oncology Laboratory, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,Wessex Clinical Genetics Service, Southampton University Hospital NHS Trust, Southampton, UK
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology, New York University School of Medicine, New York, New York, USA.,Department of Radiation Oncology, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Miquel A Pujana
- ProCURE, Oncobell, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
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9
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Raimundo L, Calheiros J, Saraiva L. Exploiting DNA Damage Repair in Precision Cancer Therapy: BRCA1 as a Prime Therapeutic Target. Cancers (Basel) 2021; 13:cancers13143438. [PMID: 34298653 PMCID: PMC8303227 DOI: 10.3390/cancers13143438] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Chemical inhibition of central DNA damage repair (DDR) proteins has become a promising approach in precision cancer therapy. In particular, BRCA1 and its DDR-associated proteins constitute important targets for developing DNA repair inhibiting drugs. This review provides relevant insights on DDR biology and pharmacology, aiming to boost the development of more effective DDR targeted therapies. Abstract Precision medicine aims to identify specific molecular alterations, such as driver mutations, allowing tailored and effective anticancer therapies. Poly(ADP)-ribose polymerase inhibitors (PARPi) are the prototypical example of targeted therapy, exploiting the inability of cancer cells to repair DNA damage. Following the concept of synthetic lethality, PARPi have gained great relevance, particularly in BRCA1 dysfunctional cancer cells. In fact, BRCA1 mutations culminate in DNA repair defects that can render cancer cells more vulnerable to therapy. However, the efficacy of these drugs has been greatly affected by the occurrence of resistance due to multi-connected DNA repair pathways that may compensate for each other. Hence, the search for additional effective agents targeting DNA damage repair (DDR) is of crucial importance. In this context, BRCA1 has assumed a central role in developing drugs aimed at inhibiting DNA repair activity. Collectively, this review provides an in-depth understanding of the biology and regulatory mechanisms of DDR pathways, highlighting the potential of DDR-associated molecules, particularly BRCA1 and its interconnected partners, in precision cancer medicine. It also affords an overview about what we have achieved and a reflection on how much remains to be done in this field, further addressing encouraging clues for the advance of DDR targeted therapy.
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10
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The BRCA1 c.788G > T (NM_007294.4) variant in a high grade serous ovarian cancer (HGSOC) patient: foods for thought. Mol Biol Rep 2021; 48:2985-2992. [PMID: 33656647 DOI: 10.1007/s11033-021-06243-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022]
Abstract
In this report we described the case of a BRCA1/2 (BRCA) molecular testing performed on tumor sample in a High Grade Serous Ovarian Cancer (HGSOC) patient with two different Next Generation Tumor Sequencing (NGTS) pipelines. The two clinical reports leaded to apparently different BRCA status, providing important foods for thought. After NGTS, the gene sequencing information (i.e., reads) are aligned to the reference gene sequences obtained from public databases, in order to provide an uniform nomenclature for unambiguous variant designation. However, the criteria adopted for variant reporting in tissue test are not always univocal. Particularly, this is the case of rare and unclassified BRCA variants for which the molecular evaluation may be a relevant challenge. Here we described a BRCA1 unclassified variant that may be re-evaluated in the context of alternative BRCA1 transcripts due to its different biological effect. We underlined that an in-depth knowledge of BRCA testing is mandatory for its appropriate use.
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11
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Cao X, Yu H, Xue J, Bai M, Zhao Y, Li Y, Zhao Y, Chen F. RNA-Primed Amplification for Noise-Suppressed Visualization of Single-Cell Splice Variants. Anal Chem 2020; 92:9356-9361. [PMID: 32456418 DOI: 10.1021/acs.analchem.0c01734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Splice variants visualization is pivotal for a deeper understanding of cell growth and development. However, it remains technically challenging due to short lengths, similar sequences, and low abundance. The existing single-cell imaging strategies suffer from nonspecific amplification that causes considerable noise during visualization of the splice variants. Herein we develop a new RNA-primed amplification strategy for noise-suppressed visualization of single-cell splice variants. Block probes were designed to specifically identify the conjugated region of exons in mRNA, which was then digested by endonuclease and provided a hydroxyl group at the 3' terminal. The RNA target can act as primer to trigger rolling circle amplification, achieving visualization of splice variants with noise suppressed to nearly zero. We further explored the expression and distribution of BRCA1 splice variants in three breast cell lines, revealing cell-type specific mapping of this cancer suppressor gene.
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Affiliation(s)
- Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Huahang Yu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Youjun Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
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12
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ISOGO: Functional annotation of protein-coding splice variants. Sci Rep 2020; 10:1069. [PMID: 31974522 PMCID: PMC6978412 DOI: 10.1038/s41598-020-57974-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/07/2020] [Indexed: 12/25/2022] Open
Abstract
The advent of RNA-seq technologies has switched the paradigm of genetic analysis from a genome to a transcriptome-based perspective. Alternative splicing generates functional diversity in genes, but the precise functions of many individual isoforms are yet to be elucidated. Gene Ontology was developed to annotate gene products according to their biological processes, molecular functions and cellular components. Despite a single gene may have several gene products, most annotations are not isoform-specific and do not distinguish the functions of the different proteins originated from a single gene. Several approaches have tried to automatically annotate ontologies at the isoform level, but this has shown to be a daunting task. We have developed ISOGO (ISOform + GO function imputation), a novel algorithm to predict the function of coding isoforms based on their protein domains and their correlation of expression along 11,373 cancer patients. Combining these two sources of information outperforms previous approaches: it provides an area under precision-recall curve (AUPRC) five times larger than previous attempts and the median AUROC of assigned functions to genes is 0.82. We tested ISOGO predictions on some genes with isoform-specific functions (BRCA1, MADD,VAMP7 and ITSN1) and they were coherent with the literature. Besides, we examined whether the main isoform of each gene -as predicted by APPRIS- was the most likely to have the annotated gene functions and it occurs in 99.4% of the genes. We also evaluated the predictions for isoform-specific functions provided by the CAFA3 challenge and results were also convincing. To make these results available to the scientific community, we have deployed a web application to consult ISOGO predictions (https://biotecnun.unav.es/app/isogo). Initial data, website link, isoform-specific GO function predictions and R code is available at https://gitlab.com/icassol/isogo.
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13
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Arason A, Agnarsson BA, Johannesdottir G, Johannsson OT, Hilmarsdottir B, Reynisdottir I, Barkardottir RB. The BRCA1 c.4096+3A>G Variant Displays Classical Characteristics of Pathogenic BRCA1 Mutations in Hereditary Breast and Ovarian Cancers, But Still Allows Homozygous Viability. Genes (Basel) 2019; 10:E882. [PMID: 31683985 PMCID: PMC6896150 DOI: 10.3390/genes10110882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/04/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
Mutations in BRCA1 result in predisposal to breast and ovarian cancers, but many variants exist with unknown clinical significance (VUS). One is BRCA1 c.4096+3A>G, which affects production of the full-length BRCA1 transcript, while augmenting transcripts lacking most or all of exon 11. Nonetheless, homozygosity of this variant has been reported in a healthy woman. We saw this variant cosegregate with breast and ovarian cancer in several family branches of four Icelandic pedigrees, with instances of phenocopies and a homozygous woman with lung cancer. We found eight heterozygous carriers (0.44%) in 1820 unselected breast cancer cases, and three (0.15%) in 1968 controls (p = 0.13). Seeking conclusive evidence, we studied tumors from carriers in the pedigrees for wild-type-loss of heterozygosity (wtLOH) and BRCA1-characteristic prevalence of estrogen receptor (ER) negativity. Of 15 breast and six ovarian tumors, wtLOH occurred in nine breast and all six ovarian tumours, and six of the nine breast tumors with wtLOH were ER-negative. These data accord with a pathogenic BRCA1-mutation. Our findings add to the current knowledge of BRCA1, and the role of its exon 11 in cancer pathogenicity, and will be of use in clinical genetic counselling.
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Affiliation(s)
- Adalgeir Arason
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Bjarni A Agnarsson
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Gudrun Johannesdottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
| | - Oskar Th Johannsson
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
- Department of Oncology, Landspitali, The National University Hospital of Iceland, 101 Reykjavik, Iceland.
| | - Bylgja Hilmarsdottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Inga Reynisdottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali - The National University Hospital of Iceland, 101 Reykjavik, Iceland.
- BMC (Biomedical Center), Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland.
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14
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Elman JS, Ni TK, Mengwasser KE, Jin D, Wronski A, Elledge SJ, Kuperwasser C. Identification of FUBP1 as a Long Tail Cancer Driver and Widespread Regulator of Tumor Suppressor and Oncogene Alternative Splicing. Cell Rep 2019; 28:3435-3449.e5. [PMID: 31553912 PMCID: PMC7297508 DOI: 10.1016/j.celrep.2019.08.060] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/10/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022] Open
Abstract
Comprehensive sequencing approaches have allowed for the identification of the most frequent contributors to cancer, known as drivers. They have also revealed a class of mutations in understudied, infrequently altered genes, referred to as "long tail" (LT) drivers. A key challenge has been to find clinically relevant LT drivers and to understand how they cooperate to drive disease. Here, we identified far upstream binding protein 1 (FUBP1) as an LT driver using an in vivo CRISPR screen. FUBP1 cooperates with other tumor suppressor genes to transform mammary epithelial cells by disrupting cellular differentiation and tissue architecture. Mechanistically, FUBP1 participates in regulating N6-methyladenosine (m6A) RNA methylation, and its loss leads to global changes in RNA splicing and widespread expression of aberrant driver isoforms. These findings suggest that somatic alteration of a single gene involved in RNA splicing and m6A methylation can produce the necessary panoply of contributors for neoplastic transformation.
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Affiliation(s)
- Jessica S Elman
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA
| | - Thomas K Ni
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA
| | - Kristen E Mengwasser
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dexter Jin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ania Wronski
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA, USA; Department of Genetics, Program in Virology, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Charlotte Kuperwasser
- Department of Developmental, Chemical and Molecular Biology, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA; Raymond & Beverly Sackler Convergence Laboratory, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA 02111, USA.
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15
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Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status. Sci Rep 2019; 9:10362. [PMID: 31316092 PMCID: PMC6637137 DOI: 10.1038/s41598-019-46652-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/28/2019] [Indexed: 12/22/2022] Open
Abstract
Non-muscle invasive bladder cancer (NMIBC) represents a crucial problem for the national health care systems due to its high rates of recurrence and the consequent need of frequent follow-ups. Here, gene expression analyses in patients diagnosed as NMIBC were performed to determine those molecular pathways involved in tumor initiation, finding that both MYC and E2F are up regulated and helps to tumor initiation and progression. Our results also support an important involvement of alternative splicing events, modifying key pathways to favour bladder tumor evolution. Finally, since MDM2 showed differential exon usage, mutations in TP53 and its protein expression have been also studied in the same patients. Our data support that recurrence is epigenetically mediated and favoured by an increase protein expression of TP53, which appears more frequently mutated in advanced stages and grades, being associated to a worse prognosis. Therefore, TP53 mutational status could be used as a potential biomarker in the first stages of NMIBC to predict recurrence and prognosis.
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16
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Li D, Harlan-Williams LM, Kumaraswamy E, Jensen RA. BRCA1-No Matter How You Splice It. Cancer Res 2019; 79:2091-2098. [PMID: 30992324 PMCID: PMC6497576 DOI: 10.1158/0008-5472.can-18-3190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/09/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
BRCA1 (breast cancer 1, early onset), a well-known breast cancer susceptibility gene, is a highly alternatively spliced gene. BRCA1 alternative splicing may serve as an alternative regulatory mechanism for the inactivation of the BRCA1 gene in both hereditary and sporadic breast cancers, and other BRCA1-associated cancers. The alternative transcripts of BRCA1 can mimic known functions, possess unique functions compared with the full-length BRCA1 transcript, and in some cases, appear to function in opposition to full-length BRCA1 In this review, we will summarize the functional "naturally occurring" alternative splicing transcripts of BRCA1 and then discuss the latest next-generation sequencing-based detection methods and techniques to detect alternative BRCA1 splicing patterns and their potential use in cancer diagnosis, prognosis, and therapy.
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Affiliation(s)
- Dan Li
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Lisa M Harlan-Williams
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Easwari Kumaraswamy
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Roy A Jensen
- The University of Kansas Cancer Center, Kansas City, Kansas.
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
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17
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Wezyk M, Szybinska A, Wojsiat J, Szczerba M, Day K, Ronnholm H, Kele M, Berdynski M, Peplonska B, Fichna JP, Ilkowski J, Styczynska M, Barczak A, Zboch M, Filipek-Gliszczynska A, Bojakowski K, Skrzypczak M, Ginalski K, Kabza M, Makalowska I, Barcikowska-Kotowicz M, Wojda U, Falk A, Zekanowski C. Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease. J Alzheimers Dis 2019; 62:175-202. [PMID: 29439343 DOI: 10.3233/jad-170830] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The BRCA1 protein, one of the major players responsible for DNA damage response has recently been linked to Alzheimer's disease (AD). Using primary fibroblasts and neurons reprogrammed from induced pluripotent stem cells (iPSC) derived from familial AD (FAD) patients, we studied the role of the BRCA1 protein underlying molecular neurodegeneration. By whole-transcriptome approach, we have found wide range of disturbances in cell cycle and DNA damage response in FAD fibroblasts. This was manifested by significantly increased content of BRCA1 phosphorylated on Ser1524 and abnormal ubiquitination and subcellular distribution of presenilin 1 (PS1). Accordingly, the iPSC-derived FAD neurons showed increased content of BRCA1(Ser1524) colocalized with degraded PS1, accompanied by an enhanced immunostaining pattern of amyloid-β. Finally, overactivation of BRCA1 was followed by an increased content of Cdc25C phosphorylated on Ser216, likely triggering cell cycle re-entry in FAD neurons. This study suggests that overactivated BRCA1 could both influence PS1 turnover leading to amyloid-β pathology and promote cell cycle re-entry-driven cell death of postmitotic neurons in AD.
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Affiliation(s)
- Michalina Wezyk
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Szybinska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Wojsiat
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcelina Szczerba
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Kelly Day
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Harriet Ronnholm
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Malin Kele
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mariusz Berdynski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland.,Department of Pharmacology and Clinical Neuroscience, Umea Universitet, Umea, Sweden
| | - Beata Peplonska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Piotr Fichna
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jan Ilkowski
- Department of Emergency Medicine, Faculty of Health Sciences, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Styczynska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Anna Barczak
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Marzena Zboch
- Center of Alzheimer's Disease of Wroclaw Medical University, Scinawa, Poland
| | - Anna Filipek-Gliszczynska
- Clinical Department of Neurology, Extrapyramidal Disorders and Alzheimer's Outpatient Clinic, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Krzysztof Bojakowski
- Clinical Department of General and Vascular Surgery, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michal Kabza
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Izabela Makalowska
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Maria Barcikowska-Kotowicz
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cezary Zekanowski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
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18
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Pettitt SJ, Lord CJ. Dissecting PARP inhibitor resistance with functional genomics. Curr Opin Genet Dev 2019; 54:55-63. [PMID: 30954761 DOI: 10.1016/j.gde.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/02/2019] [Indexed: 01/24/2023]
Abstract
The poly-(ADP-ribose) polymerase (PARP) inhibitor (PARPi) olaparib was the first licenced cancer drug that targeted an inherited form of cancer, namely ovarian cancers caused by germline BRCA1 or BRCA2 gene mutations. Multiple different PARPi have now been approved for use in a wider group of gynaecological cancers as well as for the treatment of BRCA-gene mutant breast cancer. Despite these advances, resistance to PARPi is a common clinical phenotype. Understanding, at the molecular level, how tumour cells respond to PARPi has the potential to inform how these drugs should be used clinically and since the discovery of this drug class, multiple different functional genomic strategies have been employed to dissect PARPi sensitivity and resistance. These have included genetic perturbation via classical gene targeting, gene silencing by siRNA or shRNA or transposon mutagenesis techniques. Recently, CRISPR-Cas9-based mutagenesis has greatly expanded the available range of relevant preclinical models and the precision of mutagenesis. Here, we review how these approaches have been used either in low-throughput, hypothesis-testing experiments or in the setting of large, hypothesis-generating, genetic screens aimed at understanding the molecular basis of PARPi sensitivity and resistance.
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Affiliation(s)
- Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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19
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Xie Z, Chooi JY, Toh SHM, Yang D, Basri NB, Ho YS, Chng WJ. MMSET I acts as an oncoprotein and regulates GLO1 expression in t(4;14) multiple myeloma cells. Leukemia 2018; 33:739-748. [PMID: 30470837 DOI: 10.1038/s41375-018-0300-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 06/22/2018] [Accepted: 07/05/2018] [Indexed: 12/14/2022]
Abstract
Multiple myeloma (MM) is characterized by recurrent chromosomal translocations. T(4;14) MM overexpresses multiple myeloma SET domain-containing protein (MMSET). MMSET has three major isoforms: the full-length form MMSET II and the short isoforms REIIBP and MMSET I. Here we show that the short isoform MMSET I is an oncoprotein that promoted cell survival and tumorigenesis in vitro and in vivo. Gene expression array analysis indicated that MMSET I increased glyoxalase I (GLO1) expression. Chromatin immunoprecipitation (ChIP) coupled with qPCR indicated that MMSET I bound upstream of the GLO1 transcription start site. Ectopic overexpression of MMSET I or its mutants showed MMSET I depended on its C terminus to regulate GLO1 expression. GLO1 knockdown (KD) induced apoptosis and reduced colony formation. MMSET I or GLO1 KD reduced the levels of anti-apoptosis factors such as MCL1 and BCL2. Ectopic overexpression of GLO1 resulted in the significant rescue of KMS11 cells from MMSET I KD-induced apoptosis and glycolysis inhibition. This suggested that GLO1 may be of functional importance target downstream of MMSET I. Cumulatively, our study suggests that MMSET I is an oncoprotein and potential therapeutic target for t(4;14) MM.
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Affiliation(s)
- Zhigang Xie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Jing Yuan Chooi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Sabrina Hui Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Dongxiao Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Nurhidayah Binte Basri
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, 138668, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore. .,National University Cancer Institute, National University Health System, Singapore, 119228, Singapore.
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20
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Ullah I, Sun W, Tang L, Feng J. Roles of Smads Family and Alternative Splicing Variants of Smad4 in Different Cancers. J Cancer 2018; 9:4018-4028. [PMID: 30410607 PMCID: PMC6218760 DOI: 10.7150/jca.20906] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 08/20/2018] [Indexed: 12/15/2022] Open
Abstract
Transforming Growth Factor β (TGF-β) is one of the most common secretory proteins which are recognized by membrane receptors joined to transcription regulatory factor. TGF-β signals are transduced by the Smads family that regulate differentiation, proliferation, early growth, apoptosis, homeostasis, and tumor development. Functional study of TGF-β signaling pathway and Smads role is vital for certain diseases such as cancer. Alternative splicing produces a diverse range of protein isoforms with unique function and the ability to react differently with various pharmaceutical products. This review organizes to describe the general study of Smads family, the process of alternative splicing, the general aspect of alternative splicing of Smad4 in cancer and the possible use of spliceoforms for the diagnosis and therapeutic purpose. The main aim and objective of this article are to highlight some particular mechanisms involving in alternatives splicing of cancer and also to demonstrate new evidence about alternative splicing in different steps given cancer initiation and progression.
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Affiliation(s)
- Irfan Ullah
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Weichao Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
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21
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Yang H, Jaeger M, Walker A, Wei D, Leiker K, Weitao T. Break Breast Cancer Addiction by CRISPR/Cas9 Genome Editing. J Cancer 2018; 9:219-231. [PMID: 29344267 PMCID: PMC5771328 DOI: 10.7150/jca.22554] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the leading diagnosed cancer for women globally. Evolution of breast cancer in tumorigenesis, metastasis and treatment resistance appears to be driven by the aberrant gene expression and protein degradation encoded by the cancer genomes. The uncontrolled cancer growth relies on these cellular events, thus constituting the cancerous programs and rendering the addiction towards them. These programs are likely the potential anticancer biomarkers for Personalized Medicine of breast cancer. This review intends to delineate the impact of the CRSPR/Cas-mediated genome editing in identification and validation of these anticancer biomarkers. It reviews the progress in three aspects of CRISPR/Cas9-mediated editing of the breast cancer genomes: Somatic genome editing, transcription and protein degradation addictions.
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Affiliation(s)
- Haitao Yang
- Laboratory for Cancer Genome Editing, Zhuhai Lifecode Medical Technologies. Inc. Department of Prenatal Diagnosis, Huizhou 2nd Hospital for Children and Women, #101 University Road, Tangjiawan, Zhuhai, 518900, Guangdong, China
| | - MariaLynn Jaeger
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Averi Walker
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Daniel Wei
- University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Katie Leiker
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
| | - Tao Weitao
- College of Science and Mathematics, Southwest Baptist University, 1600 University Avenue, Bolivar, Missouri 65613, USA
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22
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Liu X, Si W, Liu X, He L, Ren J, Yang Z, Yang J, Li W, Liu S, Pei F, Yang X, Sun L. JMJD6 promotes melanoma carcinogenesis through regulation of the alternative splicing of PAK1, a key MAPK signaling component. Mol Cancer 2017; 16:175. [PMID: 29187213 PMCID: PMC5708181 DOI: 10.1186/s12943-017-0744-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022] Open
Abstract
Background Melanoma, originated from melanocytes located on the basal membrane of the epithelial tissue, is the most aggressive form of skin cancer that accounts for 75% of skin cancer-related death. Although it is believed that BRAF mutation and the mitogen-activated protein kinase (MAPK) pathway play critical roles in the pathogenesis of melanoma, how the MAPK signaling is regulated in melanoma carcinogenesis is still not fully understood. Methods We characterized JMJD6 expression in melanoma tissue array by immunohistochemistry analysis. We used human melanoma A375, 451Lu and SK-MEL-1 cell lines for in vitro proliferation and invasion experiments, and xenograft transplanted mice using murine melanoma B16F10 cells by bioluminescence imaging for in vivo tumor growth and pulmonary metastasis assessments. Endothelial tube formation assay, chicken yolk sac membrane assay and matrigel plug assay were performed to test the effect of JMJD6 on the angiogenic potential in vitro and in vivo. Results Here we report that the jumonji C domain-containing demethylase/hydroxylase JMJD6 is markedly up-regulated in melanoma. We found that high expression of JMJD6 is closely correlated with advanced clinicopathologic stage, aggressiveness, and poor prognosis of melanoma. RNA-seq showed that knockdown of JMJD6 affects the alternative splicing of a panel of transcripts including that encoding for PAK1, a key component in MAPK signaling pathway. We demonstrated that JMJD6 enhances the MAPK signaling and promotes multiple cellular processes including melanogenesis, proliferation, invasion, and angiogenesis in melanoma cells. Interestingly, JMJD6 is transcriptionally activated by c-Jun, generating a feedforward loop to drive the development and progression of melanoma. Conclusions Our results indicate that JMJD6 is critically involved in melanoma carcinogenesis, supporting the pursuit of JMJD6 as a potential biomarker for melanoma aggressiveness and a target for melanoma intervention. Electronic supplementary material The online version of this article (10.1186/s12943-017-0744-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xujun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Wenzhe Si
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.,Department of Laboratory Medicine, Peking University Third Hospital, Beijing, 100191, China
| | - Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jie Ren
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ziran Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shumeng Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Fei Pei
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xiaohan Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China. .,Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 38 Xueyuan Road, Beijing, 100191, China.
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23
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Yang C, Jairam S, Amoroso KA, Robson ME, Walsh MF, Zhang L. Characterization of a novel germline BRCA1 splice variant, c.5332+4delA. Breast Cancer Res Treat 2017; 168:543-550. [PMID: 29185120 DOI: 10.1007/s10549-017-4595-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 11/22/2017] [Indexed: 12/16/2022]
Abstract
PURPOSE Germline mutations in BRCA1 and BRCA2 confer a significant increase in risk for cancer, and determining pathogenicity of a BRCA variant can guide the clinical management of the disease. About 1/3 of BRCA1 variants reported in the public databases have uncertain clinical significance due to lack of conclusive evidence. This study aims to characterize a novel BRCA1 deletion affecting the + 4 splice donor site identified in an individual with early-onset breast cancer. METHODS The effect of BRCA1 c.5332+4delA variant on RNA splicing was evaluated by amplifying regions of BRCA1 from cDNA derived from the patient. The proportion of abnormal transcript in the total transcripts was quantified. Loss of heterozygosity (LOH) in tumor tissue was investigated using Sanger sequencing and fragment analysis. RESULTS BRCA1 c.5332+4delA caused skipping of exon 21 in patient-derived samples. Semi-quantitative analysis indicated that this aberrant RT-PCR product accounts for about 40% of the total transcript levels. Loss of heterozygosity (LOH) was observed in patient's tumor tissue. CONCLUSIONS Our results indicate that the BRCA1 c.5332+4delA variant contributes to cancer predisposition through disruption of normal mRNA splicing. We classify this variant as likely pathogenic.
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Affiliation(s)
- Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Sowmya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Kimberly A Amoroso
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Michael F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA.
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24
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Hu J, Boritz E, Wylie W, Douek DC. Stochastic principles governing alternative splicing of RNA. PLoS Comput Biol 2017; 13:e1005761. [PMID: 28910283 PMCID: PMC5614656 DOI: 10.1371/journal.pcbi.1005761] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 09/26/2017] [Accepted: 09/03/2017] [Indexed: 12/18/2022] Open
Abstract
The dominance of the major transcript isoform relative to other isoforms from the same gene generated by alternative splicing (AS) is essential to the maintenance of normal cellular physiology. However, the underlying principles that determine such dominance remain unknown. Here, we analyzed the physical AS process and found that it can be modeled by a stochastic minimization process, which causes the scaled expression levels of all transcript isoforms to follow the same Weibull extreme value distribution. Surprisingly, we also found a simple equation to describe the median frequency of transcript isoforms of different dominance. This two-parameter Weibull model provides the statistical distribution of all isoforms of all transcribed genes, and reveals that previously unexplained observations concerning relative isoform expression derive from these principles. Alternative RNA splicing within eukaryotic cells enables each gene to generate multiple different mature transcripts which further encode proteins with distinct or even opposing functions. The relative frequencies of the transcript isoforms generated by a particular gene are essential to the maintenance of normal cellular physiology; however, the underlying mechanisms and principles that govern these frequencies are unknown. We analyzed the frequency distribution of all transcript isoforms in highly purified human T cell subsets and built a simple mathematical model, based on the physical process of alternative splicing, which provides statistical principles that govern this process. This model matches very well with the observed distributions of expression levels and relative frequencies of all transcript isoforms from different tissues and cell lines. Notably, we used this model to elucidate many previously unexplained observations concerning transcript isoform expression. More importantly, this model reveals the existence of simple statistical principles that can be applied to understanding an essential and complex biological process such as alternative splicing.
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Affiliation(s)
- Jianfei Hu
- Genome Analysis Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JH); (DCD)
| | - Eli Boritz
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - William Wylie
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel C. Douek
- Genome Analysis Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JH); (DCD)
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25
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Wang Y, Bernhardy AJ, Cruz C, Krais JJ, Nacson J, Nicolas E, Peri S, van der Gulden H, van der Heijden I, O'Brien SW, Zhang Y, Harrell MI, Johnson SF, Candido Dos Reis FJ, Pharoah PDP, Karlan B, Gourley C, Lambrechts D, Chenevix-Trench G, Olsson H, Benitez JJ, Greene MH, Gore M, Nussbaum R, Sadetzki S, Gayther SA, Kjaer SK, D'Andrea AD, Shapiro GI, Wiest DL, Connolly DC, Daly MB, Swisher EM, Bouwman P, Jonkers J, Balmaña J, Serra V, Johnson N. The BRCA1-Δ11q Alternative Splice Isoform Bypasses Germline Mutations and Promotes Therapeutic Resistance to PARP Inhibition and Cisplatin. Cancer Res 2017; 76:2778-90. [PMID: 27197267 DOI: 10.1158/0008-5472.can-16-0186] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/15/2016] [Indexed: 12/19/2022]
Abstract
Breast and ovarian cancer patients harboring BRCA1/2 germline mutations have clinically benefitted from therapy with PARP inhibitor (PARPi) or platinum compounds, but acquired resistance limits clinical impact. In this study, we investigated the impact of mutations on BRCA1 isoform expression and therapeutic response. Cancer cell lines and tumors harboring mutations in exon 11 of BRCA1 express a BRCA1-Δ11q splice variant lacking the majority of exon 11. The introduction of frameshift mutations to exon 11 resulted in nonsense-mediated mRNA decay of full-length, but not the BRCA1-Δ11q isoform. CRISPR/Cas9 gene editing as well as overexpression experiments revealed that the BRCA1-Δ11q protein was capable of promoting partial PARPi and cisplatin resistance relative to full-length BRCA1, both in vitro and in vivo Furthermore, spliceosome inhibitors reduced BRCA1-Δ11q levels and sensitized cells carrying exon 11 mutations to PARPi treatment. Taken together, our results provided evidence that cancer cells employ a strategy to remove deleterious germline BRCA1 mutations through alternative mRNA splicing, giving rise to isoforms that retain residual activity and contribute to therapeutic resistance. Cancer Res; 76(9); 2778-90. ©2016 AACR.
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Affiliation(s)
- Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Cristina Cruz
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain. Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Joseph Nacson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Emmanuelle Nicolas
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Suraj Peri
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | | | - Shane W O'Brien
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yong Zhang
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maribel I Harrell
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Shawn F Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Francisco J Candido Dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil. Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Beth Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Charlie Gourley
- University of Edinburgh Cancer Research UK Centre, MRC IGMM, Edinburgh, United Kingdom
| | | | | | - Håkan Olsson
- Departments of Cancer Epidemiology and Oncology, Lund University, Lund, Sweden
| | - Javier J Benitez
- Human Genetics Group and Human Genotyping Unit Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark H Greene
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Martin Gore
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Robert Nussbaum
- University of California San Francisco, Cancer Risk Program, San Francisco, California
| | - Siegal Sadetzki
- Gertner Institute for Epidemiology and Health Policy Research, Sheba Medical Center, Tel Hashomer, Israel
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Pediatrics, Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David L Wiest
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mary B Daly
- Risk Assessment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Peter Bouwman
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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26
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Tulay P, Doshi A, Serhal P, SenGupta SB. Differential expression of parental alleles of BRCA1 in human preimplantation embryos. Eur J Hum Genet 2016; 25:37-42. [PMID: 27677417 DOI: 10.1038/ejhg.2016.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 07/01/2016] [Accepted: 08/05/2016] [Indexed: 11/09/2022] Open
Abstract
Gene expression from both parental genomes is required for completion of embryogenesis. Differential methylation of each parental genome has been observed in mouse and human preimplantation embryos. It is possible that these differences in methylation affect the level of gene transcripts from each parental genome in early developing embryos. The aim of this study was to investigate if there is a parent-specific pattern of BRCA1 expression in human embryos and to examine if this affects embryo development when the embryo carries a BRCA1 or BRCA2 pathogenic mutation. Differential parental expression of ACTB, SNRPN, H19 and BRCA1 was semi-quantitatively analysed by minisequencing in 95 human preimplantation embryos obtained from 15 couples undergoing preimplantation genetic diagnosis. BRCA1 was shown to be differentially expressed favouring the paternal transcript in early developing embryos. Methylation-specific PCR showed a variable methylation profile of BRCA1 promoter region at different stages of embryonic development. Embryos carrying paternally inherited BRCA1 or 2 pathogenic variants were shown to develop more slowly compared with the embryos with maternally inherited BRCA1 or 2 pathogenic mutations. This study suggests that differential demethylation of the parental genomes can influence the early development of preimplantation embryos. Expression of maternal and paternal genes is required for the completion of embryogenesis.
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Affiliation(s)
- Pinar Tulay
- Department of Medical Genetics, Near East University, Faculty of Medicine, Yakin Dogu Bulvari, Nicosia, Cyprus. .,UCL Preimplantation Genetics Group, Institute for Women's Health, University College London, London, UK. .,4Current address: Near East University, Faculty of Medicine, Department of Medical Genetics, Yakin Dogu Bulvari, Nicosia, Cyprus., .
| | - Alpesh Doshi
- The Centre for Reproductive and Genetic Health, The New Wing Eastman Dental Hospital, London, UK
| | - Paul Serhal
- The Centre for Reproductive and Genetic Health, The New Wing Eastman Dental Hospital, London, UK
| | - Sioban B SenGupta
- Department of Medical Genetics, Near East University, Faculty of Medicine, Yakin Dogu Bulvari, Nicosia, Cyprus.,UCL Preimplantation Genetics Group, Institute for Women's Health, University College London, London, UK
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27
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Transcriptome sequencing uncovers a three-long noncoding RNA signature in predicting breast cancer survival. Sci Rep 2016; 6:27931. [PMID: 27338266 PMCID: PMC4919625 DOI: 10.1038/srep27931] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/26/2016] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play a crucial role in tumorigenesis. The aim of this study is to identify lncRNA signature that can predict breast cancer patient survival. RNA expression data from 1064 patients were downloaded from The Cancer Genome Atlas project. Cox regression, Kaplan–Meier, and receiver operating characteristic (ROC) analyses were performed to construct a model for predicting the overall survival (OS) of patients and evaluate it. A model consisting of three lncRNA genes (CAT104, LINC01234, and STXBP5-AS1) was identified. The Kaplan–Meier analysis and ROC curves proved that the model could predict the prognostic survival with good sensitivity and specificity in both the validation set (AUC = 0.752, 95% confidence intervals (CI): 0.651–0.854) and the microarray dataset (AUC = 0.714, 95%CI: 0.615–0.814). Further study showed the three-lncRNA signature was not only pervasive in different breast cancer stages, subtypes and age groups, but also provides more accurate prognostic information than some widely known biomarkers. The results suggested that RNA-seq transcriptome profiling provides that the three-lncRNA signature is an independent prognostic biomarker, and have clinical significance. In addition, lncRNA, miRNA, and mRNA interaction network indicated lncRNAs may intervene in breast cancer pathogenesis by binding to miR-190b, acting as competing endogenous RNAs.
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28
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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29
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015; 5:1137-54. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [Citation(s) in RCA: 597] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/11/2015] [Indexed: 12/14/2022]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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30
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Radulovich N, Leung L, Ibrahimov E, Navab R, Sakashita S, Zhu CQ, Kaufman E, Lockwood WW, Thu KL, Fedyshyn Y, Moffat J, Lam WL, Tsao MS. Coiled-coil domain containing 68 (CCDC68) demonstrates a tumor-suppressive role in pancreatic ductal adenocarcinoma. Oncogene 2015; 34:4238-47. [PMID: 25381825 PMCID: PMC5153324 DOI: 10.1038/onc.2014.357] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 09/09/2014] [Accepted: 09/16/2014] [Indexed: 12/26/2022]
Abstract
Using integrative genomics and functional screening, we identified coiled-coil domain containing 68 (CCDC68) as a novel putative tumor suppressor gene (TSG) in pancreatic ductal adenocarcinoma (PDAC). CCDC68 allelic losses were documented in 48% of primary PDAC patient tumors, 50% of PDAC cell lines and 30% of primary patient derived xenografts. We also discovered a single nucleotide polymorphism (SNP) variant (SNP rs1344011) that leads to exon skipping and generation of an unstable protein isoform CCDC68Δ(69-114) in 31% of PDAC patients. Overexpression of full length CCDC68 (CCDC68(wt)) in PANC-1 and Hs.766T PDAC cell lines lacking CDCC68 expression decreased proliferation and tumorigenicity in scid mice. In contrast, the downregulation of endogenous CCDC68 in MIAPaca-2 cells increased tumor growth rate. These effects were not observed with the deletion-containing isoform, CCDC68Δ(69-114).
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Affiliation(s)
- Nikolina Radulovich
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology Department, University of Toronto, Ontario, Canada
| | - Lisa Leung
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Emin Ibrahimov
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Roya Navab
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Ethan Kaufman
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - William W. Lockwood
- British Columbia Cancer Research Centre and Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Kelsie L. Thu
- British Columbia Cancer Research Centre and Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Yaroslav Fedyshyn
- Department of Molecular Genetics, Banting & Best Department of Medical Research, University of Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, Banting & Best Department of Medical Research, University of Toronto, ON, Canada
| | - Wan L. Lam
- British Columbia Cancer Research Centre and Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology Department, University of Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
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31
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Silipo M, Gautrey H, Tyson-Capper A. Deregulation of splicing factors and breast cancer development. J Mol Cell Biol 2015; 7:388-401. [PMID: 25948865 DOI: 10.1093/jmcb/mjv027] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/24/2015] [Indexed: 11/13/2022] Open
Abstract
It is well known that many genes implicated in the development and progression of breast cancer undergo aberrant alternative splicing events to produce proteins with pro-cancer properties. These changes in alternative splicing can arise from mutations or single-nucleotide polymorphisms (SNPs) within the DNA sequences of cancer-related genes, which can strongly affect the activity of splicing factors and influence the splice site choice. However, it is important to note that absence of mutations is not sufficient to prevent misleading choices in splice site selection. There is now increasing evidence to demonstrate that the expression profile of ten splicing factors (including SRs and hnRNPs) and eight RNA-binding proteins changes in breast cancer cells compared with normal cells. These modifications strongly influence the alternative splicing pattern of many cancer-related genes despite the absence of any detrimental mutations within their DNA sequences. Thus, a comprehensive assessment of the splicing factor status in breast cancer is important to provide insights into the mechanisms that lead to breast cancer development and metastasis. Whilst most studies focus on mutations that affect alternative splicing in cancer-related genes, this review focuses on splicing factors and RNA-binding proteins that are themselves deregulated in breast cancer and implicated in cancer-related alternative splicing events.
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Affiliation(s)
- Marco Silipo
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Hannah Gautrey
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alison Tyson-Capper
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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32
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Hill SJ, Clark AP, Silver DP, Livingston DM. BRCA1 pathway function in basal-like breast cancer cells. Mol Cell Biol 2014; 34:3828-42. [PMID: 25092866 PMCID: PMC4187718 DOI: 10.1128/mcb.01646-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/20/2014] [Accepted: 07/21/2014] [Indexed: 01/10/2023] Open
Abstract
Sporadic basal-like cancers (BLCs) are a common subtype of breast cancer that share multiple biological properties with BRCA1-mutated breast tumors. Despite being BRCA1(+/+), sporadic BLCs are widely viewed as phenocopies of BRCA1-mutated breast cancers, because they are hypothesized to manifest a BRCA1 functional defect or breakdown of a pathway(s) in which BRCA1 plays a major role. The role of BRCA1 in the repair of double-strand DNA breaks by homologous recombination (HR) is its best understood function and the function most often implicated in BRCA1 breast cancer suppression. Therefore, it is suspected that sporadic BLCs exhibit a defect in HR. To test this hypothesis, multiple DNA damage repair assays focused on several types of repair were performed on a group of cell lines classified as sporadic BLCs and on controls. The sporadic BLC cell lines failed to exhibit an overt HR defect. Rather, they exhibited defects in the repair of stalled replication forks, another BRCA1 function. These results provide insight into why clinical trials of poly(ADP-ribose) polymerase (PARP) inhibitors, which require an HR defect for efficacy, have been unsuccessful in sporadic BLCs, unlike cisplatin, which elicits DNA damage that requires stalled fork repair and has shown efficacy in sporadic BLCs.
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Affiliation(s)
- Sarah J Hill
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Allison P Clark
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel P Silver
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David M Livingston
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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33
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Tammaro C, Raponi M, Wilson DI, Baralle D. BRCA1 EXON 11, a CERES (composite regulatory element of splicing) element involved in splice regulation. Int J Mol Sci 2014; 15:13045-59. [PMID: 25056543 PMCID: PMC4139890 DOI: 10.3390/ijms150713045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/17/2014] [Accepted: 07/04/2014] [Indexed: 11/16/2022] Open
Abstract
Unclassified variants (UV) of BRCA1 can affect normal pre-mRNA splicing. Here, we investigate the UV c.693G>A, a "silent" change in BRCA1 exon 11, which we have found induces aberrant splicing in patient carriers and in vitro. Using a minigene assay, we show that the UV c.693G>A has a strong effect on the splicing isoform ratio of BRCA1. Systematic site-directed mutagenesis of the area surrounding the nucleotide position c.693G>A induced variable changes in the level of exon 11 inclusion/exclusion in the mRNA, pointing to the presence of a complex regulatory element with overlapping enhancer and silencer functions. Accordingly, protein binding analysis in the region detected several splicing regulatory factors involved, including SRSF1, SRSF6 and SRSF9, suggesting that this sequence represents a composite regulatory element of splicing (CERES).
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Affiliation(s)
- Claudia Tammaro
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
| | - Michela Raponi
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
| | - David I Wilson
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
| | - Diana Baralle
- Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.
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Li HD, Menon R, Omenn GS, Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet 2014; 30:340-7. [PMID: 24951248 DOI: 10.1016/j.tig.2014.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 01/17/2023]
Abstract
The vast majority of multi-exon genes in humans undergo alternative splicing, which greatly increases the functional diversity of protein species. Predicting functions at the isoform level is essential to further our understanding of developmental abnormalities and cancers, which frequently exhibit aberrant splicing and dysregulation of isoform expression. However, determination of isoform function is very difficult, and efforts to predict isoform function have been limited in the functional genomics field. Deep sequencing of RNA now provides an unprecedented amount of expression data at the transcript level. We describe here emerging computational approaches that integrate such large-scale whole-transcriptome sequencing (RNA-seq) data for predicting the functions of alternatively spliced isoforms, and we discuss their applications in developmental and cancer biology. We outline future directions for isoform function prediction, emphasizing the need for heterogeneous genomic data integration and tissue-specific, dynamic isoform-level network modeling, which will allow the field to realize its full potential.
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Affiliation(s)
- Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, MI, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, MI, USA; Department of Electrical Engineering and Computer Science, Ann Arbor, MI, USA.
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35
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Functional characterization of BRCA1 gene variants by mini-gene splicing assay. Eur J Hum Genet 2014; 22:1362-8. [PMID: 24667779 PMCID: PMC4231409 DOI: 10.1038/ejhg.2014.40] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/12/2014] [Accepted: 02/19/2014] [Indexed: 02/06/2023] Open
Abstract
Mutational screening of the breast cancer susceptibility gene BRCA1 leads to the identification of numerous pathogenic variants such as frameshift and nonsense variants, as well as large genomic rearrangements. The screening moreover identifies a large number of variants, for example, missense, silent, and intron variants, which are classified as variants of unknown clinical significance owing to the lack of causal evidence. Variants of unknown clinical significance can potentially have an impact on splicing and therefore functional examinations are warranted to classify whether these variants are pathogenic or benign. Here we validate a mini-gene splicing assay by comparing the results of 24 variants with previously published data from RT-PCR analysis on RNA from blood samples/lymphoblastoid cell lines. The analysis showed an overall concordance of 100%. In addition, we investigated 13 BRCA1 variants of unknown clinical significance or putative variants affecting splicing by in silico analysis and mini-gene splicing assay. Both the in silico analysis and mini-gene splicing assay classified six BRCA1 variants as pathogenic (c.80+1G>A, c.132C>T (p.=), c.213-1G>A, c.670+1delG, c.4185+1G>A, and c.5075-1G>C), whereas six BRCA1 variants were classified as neutral (c.-19-22_-19-21dupAT, c.302-15C>G, c.547+14delG, c.4676-20A>G, c.4987-21G>T, and c.5278-14C>G) and one BRCA1 variant remained unclassified (c.670+16G>A). In conclusion, our study emphasizes that in silico analysis and mini-gene splicing assays are important for the classification of variants, especially if no RNA is available from the patient. This knowledge is crucial for proper genetic counseling of patients and their family members.
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Raponi M, Smith LD, Silipo M, Stuani C, Buratti E, Baralle D. BRCA1 exon 11 a model of long exon splicing regulation. RNA Biol 2014; 11:351-9. [PMID: 24658338 DOI: 10.4161/rna.28458] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BRCA1 exon 11 is one of the biggest human exons, spanning 3426 bases. This gene is potentially involved in DNA repair as well as cell growth and cell cycle control. Exon 11 is regulated at the splicing level producing three main different combinations of BRCA1 mature transcripts; one including the whole of exon 11 (full isoform), one skipping the entire exon (D11 isoform), and one including only 117 base pairs of exon 11 (D11q isoform). Using minigene and deletion analyses, we have previously described important splicing regulatory sequences located at the beginning of this exon (5' end). We have now found additional important sequences located at its 3' end. In particular, we describe the presence of a strong splicing enhancer adjacent to the downstream 5' splice site, which minimizes competition from an upstream 5' splice site and so ensures long exon inclusion. Analyses of the proteins binding these RNA sequences have revealed that Tra2beta and hnRNP L are involved in the regulation of BRCA1 exon 11 by influencing the recognition of donor sites. Interestingly, BRCA1 exon 11 carrying deletion of the regulatory sequences bound by these factors also showed unexpected responses to up- or downregulation of these regulatory proteins, suggesting that they can also bind elsewhere in this large exon and elicit different effects on its recognition. The identification of sequences and proteins relevant for the regulation of BRCA1 exon 11 now provides better knowledge on how this exon is recognized and may represent an important step toward understanding how large exons are regulated.
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Affiliation(s)
| | | | - Marco Silipo
- University of Southampton; Southampton, United Kingdom
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology; Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology; Trieste, Italy
| | - Diana Baralle
- University of Southampton; Southampton, United Kingdom
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Colombo M, Blok MJ, Whiley P, Santamariña M, Gutiérrez-Enríquez S, Romero A, Garre P, Becker A, Smith LD, De Vecchi G, Brandão RD, Tserpelis D, Brown M, Blanco A, Bonache S, Menéndez M, Houdayer C, Foglia C, Fackenthal JD, Baralle D, Wappenschmidt B, Díaz-Rubio E, Caldés T, Walker L, Díez O, Vega A, Spurdle AB, Radice P, De La Hoya M. Comprehensive annotation of splice junctions supports pervasive alternative splicing at the BRCA1 locus: a report from the ENIGMA consortium. Hum Mol Genet 2014; 23:3666-80. [DOI: 10.1093/hmg/ddu075] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Mara Colombo
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands,
| | - Phillip Whiley
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia,
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia,
| | - Marta Santamariña
- Grupo de Medicina Xenómica-USC, Universidad de Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain,
| | | | - Atocha Romero
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
| | - Pilar Garre
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
| | - Alexandra Becker
- Center of Familial Breast and Ovarian Cancer, University Hospital Cologne, Cologne, Germany,
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,
| | - Lindsay Denise Smith
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK,
| | - Giovanna De Vecchi
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - Rita D. Brandão
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands,
| | - Demis Tserpelis
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands,
| | - Melissa Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia,
| | - Ana Blanco
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain,
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and
- Oncogenetics Group, Vall d'Hebron Research Institute (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain,
| | - Mireia Menéndez
- Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d'Oncologia, Barcelona, Spain,
| | - Claude Houdayer
- Service de Génétique and INSERM U830, Institut Curie and Université Paris Descartes, Sorbonne Paris Cité, Paris, France,
| | - Claudia Foglia
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - James D. Fackenthal
- Department of Medicine, The University of Chicago Medical Center, Chicago, IL, USA,
| | - Diana Baralle
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK,
| | - Barbara Wappenschmidt
- Center of Familial Breast and Ovarian Cancer, University Hospital Cologne, Cologne, Germany,
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany,
| | - Eduardo Díaz-Rubio
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
- Servicio de Oncología Médica, Hospital Clínico San Carlos, Madrid, Spain,
| | - Trinidad Caldés
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
| | - Logan Walker
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and
- Oncogenetics Group, Vall d'Hebron Research Institute (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain,
- Oncogenetics Group, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain,
| | - Amanda B. Spurdle
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia,
| | - Paolo Radice
- Department of Preventive
and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy,
| | - Miguel De La Hoya
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain,
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Tang JY, Lee JC, Hou MF, Wang CL, Chen CC, Huang HW, Chang HW. Alternative splicing for diseases, cancers, drugs, and databases. ScientificWorldJournal 2013; 2013:703568. [PMID: 23766705 PMCID: PMC3674688 DOI: 10.1155/2013/703568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/30/2013] [Indexed: 01/05/2023] Open
Abstract
Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 807, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Chueh FS, Chen YL, Hsu SC, Yang JS, Hsueh SC, Ji BC, Lu HF, Chung JG. Triptolide induced DNA damage in A375.S2 human malignant melanoma cells is mediated via reduction of DNA repair genes. Oncol Rep 2012; 29:613-8. [PMID: 23233170 DOI: 10.3892/or.2012.2170] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 11/14/2012] [Indexed: 11/05/2022] Open
Abstract
Numerous studies have demonstrated that triptolide induces cell cycle arrest and apoptosis in human cancer cell lines. However, triptolide-induced DNA damage and inhibition of DNA repair gene expression in human skin cancer cells has not previously been reported. We sought the effects of triptolide on DNA damage and associated gene expression in A375.S2 human malignant melanoma cells in vitro. Comet assay, DAPI staining and DNA gel electrophoresis were used for examining DNA damage and results indicated that triptolide induced a longer DNA migration smear based on single cell electrophoresis and DNA condensation and damage occurred based on the examination of DAPI straining and DNA gel electrophoresis. The real-time PCR technique was used to examine DNA damage and repair gene expression (mRNA) and results indicated that triptolide led to a decrease in the ataxia telangiectasia mutated (ATM), ataxia-telangiectasia and Rad3-related (ATR), breast cancer 1, early onset (BRCA-1), p53, DNA-dependent serine/threonine protein kinase (DNA-PK) and O6-methylguanine-DNA methyltransferase (MGMT) mRNA expression. Thus, these observations indicated that triptolide induced DNA damage and inhibited DNA damage and repair-associated gene expression (mRNA) that may be factors for triptolide-mediated inhibition of cell growth in vitro in A375.S2 cells.
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Affiliation(s)
- Fu-Shin Chueh
- Departments of Health and Nutrition Biotechnology, Asia University, Taichung 413, Taiwan, ROC
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