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Oh J, Pradella D, Shao C, Li H, Choi N, Ha J, Ruggiero S, Fu XD, Zheng X, Ghigna C, Shen H. Widespread Alternative Splicing Changes in Metastatic Breast Cancer Cells. Cells 2021; 10:cells10040858. [PMID: 33918758 PMCID: PMC8070448 DOI: 10.3390/cells10040858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Aberrant alternative splicing (AS) is a hallmark of cancer and a potential target for novel anti-cancer therapeutics. Breast cancer-associated AS events are known to be linked to disease progression, metastasis, and survival of breast cancer patients. To identify altered AS programs occurring in metastatic breast cancer, we perform a global analysis of AS events by using RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq). We demonstrate that, relative to low-metastatic, high-metastatic breast cancer cells show different AS choices in genes related to cancer progression. Supporting a global reshape of cancer-related splicing profiles in metastatic breast cancer we found an enrichment of RNA-binding motifs recognized by several splicing regulators, which have aberrant expression levels or activity during breast cancer progression, including SRSF1. Among SRSF1-regulated targets we found DCUN1D5, a gene for which skipping of exon 4 in its pre-mRNA introduces a premature termination codon (PTC), thus generating an unstable transcript degraded by nonsense-mediated mRNA decay (NMD). Significantly, distinct breast cancer subtypes show different DCUN1D5 isoform ratios with metastatic breast cancer expressing the highest level of the NMD-insensitive DCUN1D5 mRNA, thus showing high DCUN1D5 expression levels, which are ultimately associated with poor overall and relapse-free survival in breast cancer patients. Collectively, our results reveal global AS features of metastatic breast tumors, which open new possibilities for the treatment of these aggressive tumor types.
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Affiliation(s)
- Jagyeong Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (N.C.); (J.H.); (X.Z.)
| | - Davide Pradella
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (S.R.)
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0021, USA; (C.S.); (H.L.); (X.-D.F.)
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0021, USA; (C.S.); (H.L.); (X.-D.F.)
| | - Namjeong Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (N.C.); (J.H.); (X.Z.)
| | - Jiyeon Ha
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (N.C.); (J.H.); (X.Z.)
| | - Sonia Ruggiero
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (S.R.)
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0021, USA; (C.S.); (H.L.); (X.-D.F.)
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (N.C.); (J.H.); (X.Z.)
| | - Claudia Ghigna
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Via Abbiategrasso 207, 27100 Pavia, Italy; (D.P.); (S.R.)
- Correspondence: (C.G.); (H.S.); Tel.: +39-0382-546324 (C.G.); +82-62-715-2507 (H.S.); Fax: +39-0382-422-286 (C.G.); +82-62-715-2484 (H.S.)
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea; (J.O.); (N.C.); (J.H.); (X.Z.)
- Correspondence: (C.G.); (H.S.); Tel.: +39-0382-546324 (C.G.); +82-62-715-2507 (H.S.); Fax: +39-0382-422-286 (C.G.); +82-62-715-2484 (H.S.)
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2
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Canson D, Glubb D, Spurdle AB. Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Hum Mutat 2020; 41:1705-1721. [PMID: 32623769 DOI: 10.1002/humu.24074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
It is possible to estimate the prior probability of pathogenicity for germline disease gene variants based on bioinformatic prediction of variant effect/s. However, routinely used approaches have likely led to the underestimation and underreporting of variants located outside donor and acceptor splice site motifs that affect messenger RNA (mRNA) processing. This review presents information about hereditary cancer gene germline variants, outside native splice sites, with experimentally validated splicing effects. We list 95 exonic variants that impact splicing regulatory elements (SREs) in BRCA1, BRCA2, MLH1, MSH2, MSH6, and PMS2. We utilized a pre-existing large-scale BRCA1 functional data set to map functional SREs, and assess the relative performance of different tools to predict effects of 283 variants on such elements. We also describe rare examples of intronic variants that impact branchpoint (BP) sites and create pseudoexons. We discuss the challenges in predicting variant effect on BP site usage and pseudoexonization, and suggest strategies to improve the bioinformatic prioritization of such variants for experimental validation. Importantly, our review and analysis highlights the value of considering impact of variants outside donor and acceptor motifs on mRNA splicing and disease causation.
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Affiliation(s)
- Daffodil Canson
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Dylan Glubb
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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3
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Meulemans L, Mesman RLS, Caputo SM, Krieger S, Guillaud-Bataille M, Caux-Moncoutier V, Léone M, Boutry-Kryza N, Sokolowska J, Révillion F, Delnatte C, Tubeuf H, Soukarieh O, Bonnet-Dorion F, Guibert V, Bronner M, Bourdon V, Lizard S, Vilquin P, Privat M, Drouet A, Grout C, Calléja FMGR, Golmard L, Vrieling H, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Vreeswijk MPG, Martins A, Gaildrat P. Skipping Nonsense to Maintain Function: The Paradigm of BRCA2 Exon 12. Cancer Res 2020; 80:1374-1386. [PMID: 32046981 DOI: 10.1158/0008-5472.can-19-2491] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/18/2019] [Accepted: 02/06/2020] [Indexed: 11/16/2022]
Abstract
Germline nonsense and canonical splice site variants identified in disease-causing genes are generally considered as loss-of-function (LoF) alleles and classified as pathogenic. However, a fraction of such variants could maintain function through their impact on RNA splicing. To test this hypothesis, we used the alternatively spliced BRCA2 exon 12 (E12) as a model system because its in-frame skipping leads to a potentially functional protein. All E12 variants corresponding to putative LoF variants or predicted to alter splicing (n = 40) were selected from human variation databases and characterized for their impact on splicing in minigene assays and, when available, in patient lymphoblastoid cell lines. Moreover, a selection of variants was analyzed in a mouse embryonic stem cell-based functional assay. Using these complementary approaches, we demonstrate that a subset of variants, including nonsense variants, induced in-frame E12 skipping through the modification of splice sites or regulatory elements and, consequently, led to an internally deleted but partially functional protein. These data provide evidence, for the first time in a cancer-predisposition gene, that certain presumed null variants can retain function due to their impact on splicing. Further studies are required to estimate cancer risk associated with these hypomorphic variants. More generally, our findings highlight the need to exercise caution in the interpretation of putative LoF variants susceptible to induce in-frame splicing modifications. SIGNIFICANCE: This study presents evidence that certain presumed loss-of-function variants in a cancer predisposition gene can retain function due to their direct impact on RNA splicing.
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Affiliation(s)
- Laëtitia Meulemans
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Romy L S Mesman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Sophie Krieger
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Laboratory of Cancer Biology and Genetics, Centre François Baclesse, Caen, France.,Normandie University, UNICAEN, Caen, France
| | | | | | | | | | | | | | | | - Hélène Tubeuf
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Omar Soukarieh
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Virginie Guibert
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Myriam Bronner
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Violaine Bourdon
- Department of Genetics, Institut Paoli-Calmettes, Marseille, France
| | - Sarab Lizard
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Paul Vilquin
- Department of Pathology and Oncobiology, Montpellier University Hospital, Montpellier, France
| | - Maud Privat
- University of Clermont Auvergne, Inserm U1240, Clermont Ferrand, France.,Department of Oncogenetics, Centre Jean Perrin, Clermont Ferrand, France
| | - Aurélie Drouet
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Charlotte Grout
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France.,Inserm U830, University Paris Descartes, Paris, France
| | - Claude Houdayer
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, Institut Curie, Paris, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexandra Martins
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
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4
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Splicing regulatory factors in breast cancer hallmarks and disease progression. Oncotarget 2019; 10:6021-6037. [PMID: 31666932 PMCID: PMC6800274 DOI: 10.18632/oncotarget.27215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
By regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing events to fulfill their requirements in order to develop, progress and metastasize. However, there has been less attention for the role of the complex catalyzing the complicated multistep splicing reaction: the spliceosome. The spliceosome consists of multiple sub-complexes in total comprising 244 proteins or splice factors and 5 associated RNA molecules. Here we discuss the role of splice factors in the oncogenic processes tumors cells need to fulfill their oncogenic properties (the so-called the hallmarks of cancer). Despite the fact that splice factors have been investigated only recently, they seem to play a prominent role in already five hallmarks of cancer: angiogenesis, resisting cell death, sustaining proliferation, deregulating cellular energetics and invasion and metastasis formation by affecting major signaling pathways such as epithelial-to-mesenchymal transition, the Warburg effect, DNA damage response and hormone receptor dependent proliferation. Moreover, we could relate expression of representative genes of four other hallmarks (enabling replicative mortality, genomic instability, avoiding immune destruction and evading growth suppression) to splice factor levels in human breast cancer tumors, suggesting that also these hallmarks could be regulated by splice factors. Since many splice factors are involved in multiple hallmarks of cancer, inhibiting splice factors might provide a new layer of oncogenic control and a powerful method to combat breast cancer progression.
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5
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Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019; 103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
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6
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Çeçener G, Egeli Ü, Tunca B, şdelen İT, Tolunay Ş, Bilgel N. Importance of Novel Sequence Alterations in the FHIT Gene on Formation of Breast Cancer. TUMORI JOURNAL 2018; 93:597-603. [DOI: 10.1177/030089160709300614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aims and background The character, role and impact of FHIT gene alterations, for which recent studies have shown that the gene has a role in the early stage of carcinogenesis in breast cancer, are still unclear. Thus, the current study evaluated FHIT gene mutations from breast tissue of women with malignant and benign breast disease and to elucidate the frequency and type of mutations in this gene. Patients and methods Mutations in exons 5–9 of the FHIT gene were screened using the intronic primer pairs in 83 breast (67 malignant and 16 benign) tissue samples by single-strand conformational polymorphism and sequencing analysis. Results FHIT mutations were detected in 13 of the 67 malignant cases (19.4%) and 2 of the 16 benign cases (12.5%). Four different sequence variants were determined: two novel frame shift mutations (codon 90 insA, codon 146 delT), one intronic novel mutation (IVS8 −17 insA), and one previously identified silent transition type alteration (codon 88 C to T). In addition, determination of this silent alteration caused formation of new exonic splicing enhancer (ESE) motifs on mutated sequences by using the ESEfinder program. Conclusions Our data contribute significantly to that currently known about the presence of FHIT gene mutations on the formation of breast cancer.
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Affiliation(s)
- Gülşah Çeçener
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Ünal Egeli
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Berrin Tunca
- Department of Medical Biology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - İsmet Ta şdelen
- Department of Surgery, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Şahsine Tolunay
- Department of Pathology, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Nazan Bilgel
- Department of Family Medicine, Faculty of Medicine, Uludag University, Bursa, Turkey
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7
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Latorre E, Harries LW. Splicing regulatory factors, ageing and age-related disease. Ageing Res Rev 2017; 36:165-170. [PMID: 28456680 DOI: 10.1016/j.arr.2017.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 12/12/2022]
Abstract
Alternative splicing is a co-transcriptional process, which allows for the production of multiple transcripts from a single gene and is emerging as an important control point for gene expression. Alternatively expressed isoforms often have antagonistic function and differential temporal or spatial expression patterns, yielding enormous plasticity and adaptability to cells and increasing their ability to respond to environmental challenge. The regulation of alternative splicing is critical for numerous cellular functions in both pathological and physiological conditions, and deregulated alternative splicing is a key feature of common chronic diseases. Isoform choice is controlled by a battery of splicing regulatory proteins, which include the serine arginine rich (SRSF) proteins and the heterogeneous ribonucleoprotein (hnRNP) classes of genes. These important splicing regulators have been implicated in age-related disease, and in the ageing process itself. This review will outline the important contribution of splicing regulator proteins to ageing and age-related disease.
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8
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Kozlovski I, Siegfried Z, Amar-Schwartz A, Karni R. The role of RNA alternative splicing in regulating cancer metabolism. Hum Genet 2017; 136:1113-1127. [PMID: 28429085 DOI: 10.1007/s00439-017-1803-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
Abstract
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene. In recent years, a growing body of evidence suggests that unbalanced AS, the formation of certain pro-tumorigenic isoforms and the reduction of anti-tumorigenic isoforms, is implicated in a variety of cancers. It is becoming increasingly clear that cancer-associated AS contributes to increased growth and proliferation, partially due to effects on metabolic reprogramming. Here, we summarize the known roles of AS in regulating cancer metabolism. We present evidence supporting the idea that AS, in many types of cancer, acts as a molecular switch that alters metabolism to drive tumorigenesis. We propose that the elucidation of misregulated AS and its downstream effects on cancer metabolism emphasizes the need for new therapeutic approaches aiming to modulate the splicing machinery to selectively target cancer cells.
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Affiliation(s)
- Itamar Kozlovski
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel.
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9
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Synchronous Bilateral Breast Cancer in a Patient With Nager Syndrome. Clin Breast Cancer 2017; 17:e151-e153. [PMID: 28139434 DOI: 10.1016/j.clbc.2016.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 01/04/2023]
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10
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Wan J, Bauman JA, Graziewicz MA, Sazani P, Kole R. Oligonucleotide therapeutics in cancer. Cancer Treat Res 2016; 158:213-33. [PMID: 24222360 DOI: 10.1007/978-3-642-31659-3_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alterations in pre-mRNA splicing can have profound effects on gene expression and lead to cellular transformation. Oligonucleotide therapeutics are drugs that manipulate gene expression and improve the disease state. Antisense oligonucleotides hybridize with a target mRNA to downregulate gene expression via an RNase H-dependent mechanism. Additionally, RNase H-independent splice switching oligonucleotides (SSO) modulate alternative or aberrant splicing, to favor the therapeutically relevant splicing product. This chapter summarizes the progress made in the application of these oligonucleotide drugs in the treatment of cancer.
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Affiliation(s)
- Jing Wan
- AVI Biopharma, 3450 Monte Villa Parkway, Bothell, WA 98021, USA
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11
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Vallée MP, Di Sera TL, Nix DA, Paquette AM, Parsons MT, Bell R, Hoffman A, Hogervorst FBL, Goldgar DE, Spurdle AB, Tavtigian SV. Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants. Hum Mutat 2016; 37:627-39. [PMID: 26913838 PMCID: PMC4907813 DOI: 10.1002/humu.22973] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/29/2016] [Indexed: 01/05/2023]
Abstract
Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs—the “integrated evaluation”—that combines a sequence analysis‐based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis‐based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice‐site fitness program MaxEntScan to generate spliceogenicity‐based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity‐based probability of pathogenicity for BRCA gene single‐nucleotide substitutions. We also updated the BRCA gene Ex‐UV LOVD, available at http://hci‐exlovd.hci.utah.edu, with 77 re‐evaluable variants.
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Affiliation(s)
- Maxime P Vallée
- Department of Molecular Medicine, CHUQ Research Center, Quebec City, Canada
| | - Tonya L Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - David A Nix
- ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrew M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Russel Bell
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Hoffman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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12
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Genome-wide analysis of microRNA and mRNA expression signatures in cancer. Acta Pharmacol Sin 2015; 36:1200-11. [PMID: 26299954 DOI: 10.1038/aps.2015.67] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/22/2015] [Indexed: 12/29/2022] Open
Abstract
Cancer is an extremely diverse and complex disease that results from various genetic and epigenetic changes such as DNA copy-number variations, mutations, and aberrant mRNA and/or protein expression caused by abnormal transcriptional regulation. The expression profiles of certain microRNAs (miRNAs) and messenger RNAs (mRNAs) are closely related to cancer progression stages. In the past few decades, DNA microarray and next-generation sequencing techniques have been widely applied to identify miRNA and mRNA signatures for cancers on a genome-wide scale and have provided meaningful insights into cancer diagnosis, prognosis and personalized medicine. In this review, we summarize the progress in genome-wide analysis of miRNAs and mRNAs as cancer biomarkers, highlighting their diagnostic and prognostic roles.
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13
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Nikoshkov A, Broliden K, Attarha S, Sviatoha V, Hellström AC, Mints M, Andersson S. Expression pattern of the PRDX2, RAB1A, RAB1B, RAB5A and RAB25 genes in normal and cancer cervical tissues. Int J Oncol 2014; 46:107-12. [PMID: 25339198 DOI: 10.3892/ijo.2014.2724] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/28/2014] [Indexed: 11/06/2022] Open
Abstract
Cervical cancer is the second most prevalent malignancy among women worldwide, and additional objective diagnostic markers for this disease are needed. Given the link between cancer development and alternative splicing, we aimed to analyze the splicing patterns of the PRDX2, RAB1A, RAB1B, RAB5A and RAB25 genes, which are associated with different cancers, in normal cervical tissue, preinvasive cervical lesions and invasive cervical tumors, to identify new objective diagnostic markers. Biopsies of normal cervical tissue, preinvasive cervical lesions and invasive cervical tumors, were subjected to rapid amplification of cDNA 3' ends (3' RACE) RT‑PCR. Resulting PCR products were analyzed on agarose gels, gel‑purified and sequenced. Normal cervical tissue, preinvasive cervical lesions and invasive cervical tumors contained one PCR product corresponding to full‑length PRDX2, RAB5A and RAB25 transcripts. All tissues contained two RAB1A‑specific PCR products corresponding to the full‑length transcript and one new alternatively spliced RAB1A transcript. Invasive cervical tumors contained one PCR product corresponding to the full‑length RAB1B transcript, while all normal cervical tissue and preinvasive cervical lesions contained both the full‑length RAB1B transcript and three new alternatively spliced RAB1B transcripts. Alternative splicing of the RAB1A transcript occurs in all cervical tissues, while alternative splicing of the RAB1B transcript occurs in normal cervical tissue and in preinvasive cervical lesions; not in invasive cervical tumors.
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Affiliation(s)
- Andrej Nikoshkov
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institute, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
| | - Kristina Broliden
- Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Sanaz Attarha
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institute, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
| | - Vitali Sviatoha
- Department of Oncology‑Pathology, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Ann-Cathrin Hellström
- Department of Gynecological Oncology, Radiumhemmet, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Miriam Mints
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institute, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
| | - Sonia Andersson
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institute, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden
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14
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Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nature 2014; 513:120-3. [PMID: 25141179 PMCID: PMC4156553 DOI: 10.1038/nature13695] [Citation(s) in RCA: 253] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/18/2014] [Indexed: 12/13/2022]
Abstract
Saturation mutagenesis1,2 – coupled to an appropriate biological assay – represents a fundamental means of achieving a high-resolution understanding of regulatory3 and protein-coding4 nucleic acid sequences of interest. However, mutagenized sequences introduced in trans on episomes or via random or “safe-harbor” integration fail to capture the native context of the endogenous chromosomal locus5. This shortcoming markedly limits the interpretability of the resulting measurements of mutational impact. Here, we couple CRISPR/Cas9 RNA-guided cleavage6 with multiplex homology-directed repair (HDR) using a complex library of donor templates to demonstrate saturation editing of genomic regions. In exon 18 of BRCA1, we replace a six base-pair (bp) genomic region with all possible hexamers, or the full exon with all possible single nucleotide variants (SNVs), and measure strong effects on transcript abundance attributable to nonsense-mediated decay and exonic splicing elements. We similarly perform saturation genome editing of a well-conserved coding region of an essential gene, DBR1, and measure relative effects on growth that correlate with functional impact. Measurement of the functional consequences of large numbers of mutations with saturation genome editing will potentially facilitate high-resolution functional dissection of both cis-regulatory elements and trans-acting factors, as well as the interpretation of variants of uncertain significance observed in clinical sequencing.
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Affiliation(s)
- Gregory M Findlay
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2]
| | - Evan A Boyle
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2]
| | - Ronald J Hause
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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15
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Addiction to multiple oncogenes can be exploited to prevent the emergence of therapeutic resistance. Proc Natl Acad Sci U S A 2014; 111:E3316-24. [PMID: 25071175 DOI: 10.1073/pnas.1406123111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many cancers exhibit sensitivity to the inhibition of a single genetic lesion, a property that has been successfully exploited with oncogene-targeted therapeutics. However, inhibition of single oncogenes often fails to result in sustained tumor regression due to the emergence of therapy-resistant cells. Here, we report that MYC-driven lymphomas frequently acquire activating mutations in β-catenin, including a previously unreported mutation in a splice acceptor site. Tumors with these genetic lesions are highly dependent on β-catenin for their survival and the suppression of β-catenin resulted in marked apoptosis causally related to a decrease in Bcl-xL expression. Using a novel inducible inhibitor of β-catenin, we illustrate that, although MYC withdrawal or β-catenin inhibition alone results in initial tumor regression, most tumors ultimately recurred, mimicking the clinical response to single-agent targeted therapy. Importantly, the simultaneous combined inhibition of both MYC and β-catenin promoted more rapid tumor regression and successfully prevented tumor recurrence. Hence, we demonstrated that MYC-induced tumors are addicted to mutant β-catenin, and the combined inactivation of MYC and β-catenin induces sustained tumor regression. Our results provide a proof of principle that targeting multiple oncogene addicted pathways can prevent therapeutic resistance.
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16
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Vandevenne M, O'Connell MR, Helder S, Shepherd NE, Matthews JM, Kwan AH, Segal DJ, Mackay JP. Engineering Specificity Changes on a RanBP2 Zinc Finger that Binds Single-Stranded RNA. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Vandevenne M, O'Connell MR, Helder S, Shepherd NE, Matthews JM, Kwan AH, Segal DJ, Mackay JP. Engineering specificity changes on a RanBP2 zinc finger that binds single-stranded RNA. Angew Chem Int Ed Engl 2014; 53:7848-52. [PMID: 25044781 DOI: 10.1002/anie.201402980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Indexed: 12/13/2022]
Abstract
The realization that gene transcription is much more pervasive than previously thought and that many diverse RNA species exist in simple as well as complex organisms has triggered efforts to develop functionalized RNA-binding proteins (RBPs) that have the ability to probe and manipulate RNA function. Previously, we showed that the RanBP2-type zinc finger (ZF) domain is a good candidate for an addressable single-stranded-RNA (ssRNA) binding domain that can recognize ssRNA in a modular and specific manner. In the present study, we successfully engineered a sequence specificity change onto this ZF scaffold by using a combinatorial approach based on phage display. This work constitutes a foundation from which a set of RanBP2 ZFs might be developed that is able to recognize any given RNA sequence.
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Affiliation(s)
- Marylène Vandevenne
- School of Molecular Bioscience, University of Sydney, Sydney, N.S.W 2006 (Australia)
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18
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RNA splicing: a new player in the DNA damage response. Int J Cell Biol 2013; 2013:153634. [PMID: 24159334 PMCID: PMC3789447 DOI: 10.1155/2013/153634] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 12/16/2022] Open
Abstract
It is widely accepted that tumorigenesis is a multistep process characterized by the sequential accumulation of genetic alterations. However, the molecular basis of genomic instability in cancer is still partially understood. The observation that hereditary cancers are often characterized by mutations in DNA repair and checkpoint genes suggests that accumulation of DNA damage is a major contributor to the oncogenic transformation. It is therefore of great interest to identify all the cellular pathways that contribute to the response to DNA damage. Recently, RNA processing has emerged as a novel pathway that may contribute to the maintenance of genome stability. In this review, we illustrate several different mechanisms through which pre-mRNA splicing and genomic stability can influence each other. We specifically focus on the role of splicing factors in the DNA damage response and describe how, in turn, activation of the DDR can influence the activity of splicing factors.
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19
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Juárez-Méndez S, Zentella-Dehesa A, Villegas-Ruíz V, Pérez-González OA, Salcedo M, López-Romero R, Román-Basaure E, Lazos-Ochoa M, Montes de Oca-Fuentes VE, Vázquez-Ortiz G, Moreno J. Splice variants of zinc finger protein 695 mRNA associated to ovarian cancer. J Ovarian Res 2013; 6:61. [PMID: 24007497 PMCID: PMC3847372 DOI: 10.1186/1757-2215-6-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/24/2013] [Indexed: 12/22/2022] Open
Abstract
Background Studies of alternative mRNA splicing (AS) in health and disease have yet to yield the complete picture of protein diversity and its role in physiology and pathology. Some forms of cancer appear to be associated to certain alternative mRNA splice variants, but their role in the cancer development and outcome is unclear. Methods We examined AS profiles by means of whole genome exon expression microarrays (Affymetrix GeneChip 1.0) in ovarian tumors and ovarian cancer-derived cell lines, compared to healthy ovarian tissue. Alternatively spliced genes expressed predominantly in ovarian tumors and cell lines were confirmed by RT-PCR. Results Among several significantly overexpressed AS genes in malignant ovarian tumors and ovarian cancer cell lines, the most significant one was that of the zinc finger protein ZNF695, with two previously unknown mRNA splice variants identified in ovarian tumors and cell lines. The identity of ZNF695 AS variants was confirmed by cloning and sequencing of the amplicons obtained from ovarian cancer tissue and cell lines. Conclusions Alternative ZNF695 mRNA splicing could be a marker of ovarian cancer with possible implications on its pathogenesis.
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20
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Liu S, Cheng C. Alternative RNA splicing and cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2013; 4:547-66. [PMID: 23765697 PMCID: PMC4426271 DOI: 10.1002/wrna.1178] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 05/10/2013] [Accepted: 05/11/2013] [Indexed: 01/04/2023]
Abstract
Alternative splicing of pre-messenger RNA (mRNA) is a fundamental mechanism by which a gene can give rise to multiple distinct mRNA transcripts, yielding protein isoforms with different, even opposing, functions. With the recognition that alternative splicing occurs in nearly all human genes, its relationship with cancer-associated pathways has emerged as a rapidly growing field. In this review, we summarize recent findings that have implicated the critical role of alternative splicing in cancer and discuss current understandings of the mechanisms underlying dysregulated alternative splicing in cancer cells.
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Affiliation(s)
- Sali Liu
- Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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21
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Ghigna C, Riva S, Biamonti G. Alternative splicing of tumor suppressors and oncogenes. Cancer Treat Res 2013; 158:95-117. [PMID: 24222355 DOI: 10.1007/978-3-642-31659-3_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Alternative splicing is a fundamental mechanism to modulate gene expression programs in response to different growth and environmental stimuli. There is now ample evidence that alternative splicing errors, caused by mutations in cis-acting elements and defects and/or imbalances in trans-acting factors, may be causatively associated to cancer progression. Recent work indicates the existence of an intricate network of interactions between alternative splicing events and signal transduction pathways. In this network, splicing factors occupy a central position and appear to function both as targets and effectors of regulatory circuits. Thus, a change in their activity deeply affects alternative splicing profiles and hence the cell behavior. Here, we discuss a number of cases that exemplify the involvement of deregulated alternative splicing in tumor progression.
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Affiliation(s)
- Claudia Ghigna
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, 27100, Italy
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22
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Abstract
For most of our 25,000 genes, the removal of introns by pre-messenger RNA (pre-mRNA) splicing represents an essential step toward the production of functional messenger RNAs (mRNAs). Alternative splicing of a single pre-mRNA results in the production of different mRNAs. Although complex organisms use alternative splicing to expand protein function and phenotypic diversity, patterns of alternative splicing are often altered in cancer cells. Alternative splicing contributes to tumorigenesis by producing splice isoforms that can stimulate cell proliferation and cell migration or induce resistance to apoptosis and anticancer agents. Cancer-specific changes in splicing profiles can occur through mutations that are affecting splice sites and splicing control elements, and also by alterations in the expression of proteins that control splicing decisions. Recent progress in global approaches that interrogate splicing diversity should help to obtain specific splicing signatures for cancer types. The development of innovative approaches for annotating and reprogramming splicing events will more fully establish the essential contribution of alternative splicing to the biology of cancer and will hopefully provide novel targets and anticancer strategies. Metazoan genes are usually made up of several exons interrupted by introns. The introns are removed from the pre-mRNA by RNA splicing. In conjunction with other maturation steps, such as capping and polyadenylation, the spliced mRNA is then transported to the cytoplasm to be translated into a functional protein. The basic mechanism of splicing requires accurate recognition of each extremity of each intron by the spliceosome. Introns are identified by the binding of U1 snRNP to the 5' splice site and the U2AF65/U2AF35 complex to the 3' splice site. Following these interactions, other proteins and snRNPs are recruited to generate the complete spliceosomal complex needed to excise the intron. While many introns are constitutively removed by the spliceosome, other splice junctions are not used systematically, generating the phenomenon of alternative splicing. Alternative splicing is therefore the process by which a single species of pre-mRNA can be matured to produce different mRNA molecules (Fig. 1). Depending on the number and types of alternative splicing events, a pre-mRNA can generate from two to several thousands different mRNAs leading to the production of a corresponding number of proteins. It is now believed that the expression of at least 70 % of human genes is subjected to alternative splicing, implying an enormous contribution to proteomic diversity, and by extension, to the development and the evolution of complex animals. Defects in splicing have been associated with human diseases (Caceres and Kornblihtt, Trends Genet 18(4):186-93, 2002, Cartegni et al., Nat Rev Genet 3(4):285-98, 2002, Pagani and Baralle, Nat Rev Genet 5(5):389-96, 2004), including cancer (Brinkman, Clin Biochem 37(7):584-94, 2004, Venables, Bioessays 28(4):378-86, 2006, Srebrow and Kornblihtt, J Cell Sci 119(Pt 13):2635-2641, 2006, Revil et al., Bull Cancer 93(9):909-919, 2006, Venables, Transworld Res Network, 2006, Pajares et al., Lancet Oncol 8(4):349-57, 2007, Skotheim and Nees, Int J Biochem Cell Biol 39:1432-1449, 2007). Numerous studies have now confirmed the existence of specific differences in the alternative splicing profiles between normal and cancer tissues. Although there are a few cases where specific mutations are the primary cause for these changes, global alterations in alternative splicing in cancer cells may be primarily derived from changes in the expression of RNA-binding proteins that control splice site selection. Overall, these cancer-specific differences in alternative splicing offer an immense potential to improve the diagnosis and the prognosis of cancer. This review will focus on the functional impact of cancer-associated alternative splicing variants, the molecular determinants that alter the splicing decisions in cancer cells, and future therapeutic strategies.
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23
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Antoniou AC, Kuchenbaecker KB, Soucy P, Beesley J, Chen X, McGuffog L, Lee A, Barrowdale D, Healey S, Sinilnikova OM, Caligo MA, Loman N, Harbst K, Lindblom A, Arver B, Rosenquist R, Karlsson P, Nathanson K, Domchek S, Rebbeck T, Jakubowska A, Lubinski J, Jaworska K, Durda K, Złowowcka-Perłowska E, Osorio A, Durán M, Andrés R, Benítez J, Hamann U, Hogervorst FB, van Os TA, Verhoef S, Meijers-Heijboer HEJ, Wijnen J, Gómez Garcia EB, Ligtenberg MJ, Kriege M, Collée JM, Ausems MGEM, Oosterwijk JC, Peock S, Frost D, Ellis SD, Platte R, Fineberg E, Evans DG, Lalloo F, Jacobs C, Eeles R, Adlard J, Davidson R, Cole T, Cook J, Paterson J, Douglas F, Brewer C, Hodgson S, Morrison PJ, Walker L, Rogers MT, Donaldson A, Dorkins H, Godwin AK, Bove B, Stoppa-Lyonnet D, Houdayer C, Buecher B, de Pauw A, Mazoyer S, Calender A, Léoné M, Bressac- de Paillerets B, Caron O, Sobol H, Frenay M, Prieur F, Ferrer SF, Mortemousque I, Buys S, Daly M, Miron A, Terry MB, Hopper JL, John EM, Southey M, Goldgar D, Singer CF, Fink-Retter A, Tea MK, Kaulich DG, Hansen TVO, Nielsen FC, Barkardottir RB, Gaudet M, Kirchhoff T, Joseph V, Dutra-Clarke A, Offit K, Piedmonte M, Kirk J, Cohn D, Hurteau J, Byron J, Fiorica J, Toland AE, Montagna M, Oliani C, Imyanitov E, Isaacs C, Tihomirova L, Blanco I, Lazaro C, Teulé A, Valle JD, Gayther SA, Odunsi K, Gross J, Karlan BY, Olah E, Teo SH, Ganz PA, Beattie MS, Dorfling CM, van Rensburg EJ, Diez O, Kwong A, Schmutzler RK, Wappenschmidt B, Engel C, Meindl A, Ditsch N, Arnold N, Heidemann S, Niederacher D, Preisler-Adams S, Gadzicki D, Varon-Mateeva R, Deissler H, Gehrig A, Sutter C, Kast K, Fiebig B, Schäfer D, Caldes T, de la Hoya M, Nevanlinna H, Muranen TA, Lespérance B, Spurdle AB, Neuhausen SL, Ding YC, Wang X, Fredericksen Z, Pankratz VS, Lindor NM, Peterlongo P, Manoukian S, Peissel B, Zaffaroni D, Bonanni B, Bernard L, Dolcetti R, Papi L, Ottini L, Radice P, Greene MH, Loud JT, Andrulis IL, Ozcelik H, Mulligan AM, Glendon G, Thomassen M, Gerdes AM, Jensen UB, Skytte AB, Kruse TA, Chenevix-Trench G, Couch FJ, Simard J, Easton DF. Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. Breast Cancer Res 2012; 14:R33. [PMID: 22348646 PMCID: PMC3496151 DOI: 10.1186/bcr3121] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 11/15/2011] [Accepted: 02/20/2012] [Indexed: 01/15/2023] Open
Abstract
INTRODUCTION Several common alleles have been shown to be associated with breast and/or ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Recent genome-wide association studies of breast cancer have identified eight additional breast cancer susceptibility loci: rs1011970 (9p21, CDKN2A/B), rs10995190 (ZNF365), rs704010 (ZMIZ1), rs2380205 (10p15), rs614367 (11q13), rs1292011 (12q24), rs10771399 (12p11 near PTHLH) and rs865686 (9q31.2). METHODS To evaluate whether these single nucleotide polymorphisms (SNPs) are associated with breast cancer risk for BRCA1 and BRCA2 carriers, we genotyped these SNPs in 12,599 BRCA1 and 7,132 BRCA2 mutation carriers and analysed the associations with breast cancer risk within a retrospective likelihood framework. RESULTS Only SNP rs10771399 near PTHLH was associated with breast cancer risk for BRCA1 mutation carriers (per-allele hazard ratio (HR) = 0.87, 95% CI: 0.81 to 0.94, P-trend = 3 × 10-4). The association was restricted to mutations proven or predicted to lead to absence of protein expression (HR = 0.82, 95% CI: 0.74 to 0.90, P-trend = 3.1 × 10-5, P-difference = 0.03). Four SNPs were associated with the risk of breast cancer for BRCA2 mutation carriers: rs10995190, P-trend = 0.015; rs1011970, P-trend = 0.048; rs865686, 2df-P = 0.007; rs1292011 2df-P = 0.03. rs10771399 (PTHLH) was predominantly associated with estrogen receptor (ER)-negative breast cancer for BRCA1 mutation carriers (HR = 0.81, 95% CI: 0.74 to 0.90, P-trend = 4 × 10-5) and there was marginal evidence of association with ER-negative breast cancer for BRCA2 mutation carriers (HR = 0.78, 95% CI: 0.62 to 1.00, P-trend = 0.049). CONCLUSIONS The present findings, in combination with previously identified modifiers of risk, will ultimately lead to more accurate risk prediction and an improved understanding of the disease etiology in BRCA1 and BRCA2 mutation carriers.
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Affiliation(s)
- Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Karoline B Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec, 2705 Laurier Boulevard, T3-57, Quebec City, QC Canada
| | - Jonathan Beesley
- Genetics and Population Health Division, Queensland Institute of Medical Research, 300 Herston Rd, Herston, Brisbane, QLD 4006, Australia
| | - Xiaoqing Chen
- Genetics and Population Health Division, Queensland Institute of Medical Research, 300 Herston Rd, Herston, Brisbane, QLD 4006, Australia
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Sue Healey
- Genetics and Population Health Division, Queensland Institute of Medical Research, 300 Herston Rd, Herston, Brisbane, QLD 4006, Australia
| | - Olga M Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Centre Hospitalier Universitaire de Lyon/Centre Léon Bérard, 28 rue Laënnec, Lyon 69373, France and INSERM U1052, CNRS UMR5286, Université Lyon 1, Cancer Research Center of Lyon, 28 rue Laënnec, Lyon 69373, France
| | - Maria A Caligo
- Section of Genetic Oncology, Dept. of Laboratory Medicine, University and University Hospital of Pisa, Via Roma 57, 56125 Pisa, Italy
| | - Niklas Loman
- Department of Oncology, Lund University Hospital, Lund, Sweden
| | - Katja Harbst
- Department of Oncology, Lund University Hospital, Lund, Sweden
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Brita Arver
- Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Karlsson
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kate Nathanson
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Susan Domchek
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tim Rebbeck
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin and Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | | | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain and Spanish Network on Rare Diseases (CIBERER)
| | - Mercedes Durán
- Institute of Biology and Molecular Genetics. Universidad de Valladolid (IBGM-UVA), Valladolid, Spain
| | - Raquel Andrés
- Oncology unit. Hospital clinico Universitario "Lozano Blesa", Zaragoza, Spain
| | - Javier Benítez
- Human Genetics Group and Genotyping Unit, Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain and Spanish Network on Rare Diseases (CIBERER)
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Frans B Hogervorst
- Family Cancer Clinic, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Theo A van Os
- Department of Clinical Genetics, Academic Meical Center, Amsterdam, The Netherlands
| | - Senno Verhoef
- Department of Clinical Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Juul Wijnen
- Department of Clinical Genetics and GROM, School for Oncology and Developmental Biology, MUMC, Maastricht, The Netherlands
| | - Encarna B Gómez Garcia
- Department of Clinical Genetics and GROM, School for Oncology and Developmental Biology, MUMC, Maastricht, The Netherlands
| | - Marjolijn J Ligtenberg
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Mieke Kriege
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - J Margriet Collée
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Margreet GEM Ausems
- Department of Medical Genetics, University Medical Center Utrecht, PO Box 85090, 3508 AB Utrecht, The Netherlands
| | - Jan C Oosterwijk
- Department of Genetics, University Medical Center, Groningen University, Groningen, The Netherlands
| | - Susan Peock
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Steve D Ellis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Radka Platte
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Elena Fineberg
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - D Gareth Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Chris Jacobs
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Ros Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, UK
| | | | - Rosemarie Davidson
- Ferguson-Smith Centre for Clinical Genetics, Yorkhill Hospitals, Glasgow, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's Hospital Healthcare NHS Trust, Edgbaston, Birmingham, UK
| | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, UK
| | - Joan Paterson
- Department of Clinical Genetics, East Anglian Regional Genetics Service, Addenbrookes Hospital, Cambridge, UK
| | - Fiona Douglas
- Institute of Genetic Medicine, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon & Exeter Hospital, Exeter, UK
| | - Shirley Hodgson
- Medical Genetics Unit, St George's, University of London, UK
| | - Patrick J Morrison
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, and Department of Medical Genetics, Queens University Belfast, Belfast UK
| | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, UK
| | - Mark T Rogers
- All Wales Medical Genetics Services, University Hospital of Wales, Cardiff, UK
| | - Alan Donaldson
- Clinical Genetics Department, St Michael's Hospital, Bristol, UK
| | - Huw Dorkins
- North West Thames Regional Genetics Service, Kennedy-Galton Centre, Harrow, UK
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Betsy Bove
- Clinical Molecular Genetics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Dominique Stoppa-Lyonnet
- Service de Génétique Oncologique, Institut Curie, Paris, France, Unité INSERM U830, Institut Curie, Paris, France, Université Paris Descartes, Faculté de Médecine, Paris, France
| | - Claude Houdayer
- Service de Génétique Oncologique, Institut Curie, Paris, France and Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Bruno Buecher
- Service de Génétique Oncologique, Institut Curie, 26 rue d'Ulm, Paris, France
| | - Antoine de Pauw
- Service de Génétique Oncologique, Institut Curie, Paris, France
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Alain Calender
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Mélanie Léoné
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Brigitte Bressac- de Paillerets
- Service de Génétique, Institut de Cancérologie Gustave Roussy, Villejuif, France and INSERM U946, Fondation Jean Dausset, Paris, France
| | - Olivier Caron
- Consultation de Génétique, Département de Médecine, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Hagay Sobol
- Département Oncologie génétique, Prévention et Dépistage, INSERM CIC-P9502, Institut Paoli-Calmettes/Université d'Aix-Marseille II, Marseille, France
| | | | - Fabienne Prieur
- Service de Génétique Clinique Chromosomique et Moléculaire, Centre Hospitalier Universitaire de St Etienne, St Etienne, France
| | - Sandra Fert Ferrer
- Laboratoire de Génétique Chromosomique, Hôtel Dieu Centre Hospitalier, BP 1125 Chambéry, France
| | | | - Saundra Buys
- Huntsman Cancer Institute, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Mary Daly
- Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Alexander Miron
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Surgery, Harvard Medical School, 27 Drydock Avenue, Boston, MA 02210, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University, New York, NY, USA
| | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic (MEGA) Epidemiology, Melbourne School of Population Health, Level 1, 723 Swanston Street, The University of Melbourne, VIC 3010, Australia
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, 2201 Walnut Avenue, Suite 300, Fremont, CA 94538, USA
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Australia
| | - David Goldgar
- Department of Dermatology, University of Utah School of Medicine, 30 North 1900 East, SOM 4B454, Salt Lake City, UT 84132, USA
| | - Christian F Singer
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Anneliese Fink-Retter
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Muy-Kheng Tea
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | | | - Thomas VO Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali - University Hospital, Reykjavik Iceland and Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Mia Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Tomas Kirchhoff
- Department of Environmental Medicine, NYU Cancer Institute, New York University School of Medicine, New York, NY, USA
| | - Vijai Joseph
- Clinical Cancer Genetics Laboratory, Memorial Sloane Kettering Cancer Center, New York, NY, USA
| | - Ana Dutra-Clarke
- Clinical Cancer Genetics Laboratory, Memorial Sloane Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Clinical Cancer Genetics Laboratory, Memorial Sloane Kettering Cancer Center, New York, NY, USA
| | - Marion Piedmonte
- Statistical and Data Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Judy Kirk
- Australia New Zealand (ANZGOG), Westmead Hospital, Sydney, Australia
| | - David Cohn
- Ohio State University, Columbus Cancer Council, Columbus, OH, USA
| | - Jean Hurteau
- Evanston CCOP - NorthShore University Health System; University of Chicago, Chicago, IL, USA
| | - John Byron
- Southern Pines Women's Health Center, P.C., University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James Fiorica
- Sarasota Memorial Healthcare, Tufts Medical Center, Sarasota, Florida, USA
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | | | - Evgeny Imyanitov
- Laboratory of Molecular Oncology, N.N. Petrov Institute of Oncology, St.-Petersburg, Russia
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
| | | | - Ignacio Blanco
- Genetic Counselling Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Alex Teulé
- Genetic Counselling Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - J Del Valle
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jenny Gross
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute at Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute at Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Malaysia and University Malaya Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Patricia A Ganz
- Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, CA, USA
| | - Mary S Beattie
- UCSF Cancer Risk Program, University of California, San Francisco, CA; UCSF Departments of Medicine, Epidemiology, and Biostatistics, Sand Francisco, CA, USA
| | - Cecelia M Dorfling
- Cancer Genetics Laboratory, Department of Genetics, University of Pretoria, South Africa
| | | | - Orland Diez
- Oncogenetics Laboratory. Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital. Barcelona, Spain
| | - Ava Kwong
- The Hong Kong Hereditary Breast Cancer Family Registry; The Universtiy of Hong Kong; Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong
| | - Rita K Schmutzler
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), University hospital of Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), University hospital of Cologne, Cologne, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Alfons Meindl
- Department of Gynaecology and Obstetrics, Division of Tumour Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Nina Ditsch
- Department of Gynaecology and Obstetrics, Ludwig-Maximilian University Munich, Munich, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Simone Heidemann
- Institute of Human Genetics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Dieter Niederacher
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Dorothea Gadzicki
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
| | | | - Helmut Deissler
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Germany
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University Würzburg, Würzburg, Germany
| | - Christian Sutter
- Institute of Human Genetics, Department of Human Genetics, University Hospital Heidelberg, Germany
| | - Karin Kast
- Department of Gynaecology and Obstetrics, University Hospital Carl Gustav Carus, Technical University. Dresden, Germany
| | - Britta Fiebig
- Institute of Human Genetics, University Regensburg, Regensbirg. Germany
| | - Dieter Schäfer
- Institute of Human Genetics, University Hospital Frankfurt a.M., Germany Molecular Oncology Laboratory, Hospital Clinico San Carlos, Madrid, Spain
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, Martin Lagos s/n, Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, Martin Lagos s/n, Madrid, Spain
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Biomedicum Helsinki, P.O. BOX 700, 00029 HUS, Helsinki, Finland
| | - Taru A Muranen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Biomedicum Helsinki, P.O. BOX 700, 00029 HUS, Helsinki, Finland
| | - Bernard Lespérance
- Faculty of Medicine - Medicine and Medical Specialties, Université de Montréal Hemato-oncology service, Hôpital du Sacré-Coeur de Montréal, 5400 Gouin Blvd West Montreal, QC, Canada
| | - Amanda B Spurdle
- Genetics and Population Health Division, Queensland Institute of Medical Research, 300 Herston Rd, Herston, Brisbane, QLD 4006, Australia
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Yuan C Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine, Fondazione IRCCS Istituto Nazionale Tumouri (INT), Milan, Italy and IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumouri (INT), Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumouri (INT), Milan, Italy
| | - Daniela Zaffaroni
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumouri (INT), Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy and Consortium for Genomics Technology (Cogentech), Milan, Italy
| | - Riccardo Dolcetti
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, Aviano (PN), Italy
| | - Laura Papi
- Medical Genetics Unit, Department of Clinical Physiopathology, University of Florence, Firenze, Italy
| | - Laura Ottini
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine, Fondazione IRCCS Istituto Nazionale Tumouri (INT), Milan, Italy and IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Mark H Greene
- Clinical Genetics Branch, DCEG, NCI; Room EPS 7032, Rockville, MD 20852, USA
| | - Jennifer T Loud
- Clinical Genetics Branch, DCEG, NCI; Room EPS 7032, Rockville, MD 20852, USA
| | - Irene L Andrulis
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON; Cancer Care Ontario, Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
| | - Hilmi Ozcelik
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON; Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine, and the Keenan Research Centre of the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Gord Glendon
- Ontario Cancer Genetics Network: Cancer Care Ontario, Toronto, ON, Canada
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Denmark
| | - Anne-Marie Gerdes
- Department of Clincial Genetics, Rigshospital and Copenhagen University, Denmark
| | - Uffe B Jensen
- Department of Clinical Genetics, Skejby Hospital, Aarhus, Denmark
| | | | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Denmark
| | - Georgia Chenevix-Trench
- Genetics and Population Health Division, Queensland Institute of Medical Research, 300 Herston Rd, Herston, Brisbane, QLD 4006, Australia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec, 2705 Laurier Boulevard, T3-57, Quebec City and Canada Research Chair in Oncogenetics, Department of Molecular Medicine, Faculty of Medicine, Laval University, QC, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
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Bolton KL, Chenevix-Trench G, Goh C, Sadetzki S, Ramus SJ, Karlan BY, Lambrechts D, Despierre E, Barrowdale D, McGuffog L, Healey S, Easton DF, Sinilnikova O, Benítez J, García MJ, Neuhausen S, Gail MH, Hartge P, Peock S, Frost D, Evans DG, Eeles R, Godwin AK, Daly MB, Kwong A, Ma ESK, Lázaro C, Blanco I, Montagna M, D'Andrea E, Nicoletto MO, Johnatty SE, Kjær SK, Jensen A, Høgdall E, Goode EL, Fridley BL, Loud JT, Greene MH, Mai PL, Chetrit A, Lubin F, Hirsh-Yechezkel G, Glendon G, Andrulis IL, Toland AE, Senter L, Gore ME, Gourley C, Michie CO, Song H, Tyrer J, Whittemore AS, McGuire V, Sieh W, Kristoffersson U, Olsson H, Borg Å, Levine DA, Steele L, Beattie MS, Chan S, Nussbaum RL, Moysich KB, Gross J, Cass I, Walsh C, Li AJ, Leuchter R, Gordon O, Garcia-Closas M, Gayther SA, Chanock SJ, Antoniou AC, Pharoah PDP. Association between BRCA1 and BRCA2 mutations and survival in women with invasive epithelial ovarian cancer. JAMA 2012; 307:382-90. [PMID: 22274685 PMCID: PMC3727895 DOI: 10.1001/jama.2012.20] [Citation(s) in RCA: 478] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT Approximately 10% of women with invasive epithelial ovarian cancer (EOC) carry deleterious germline mutations in BRCA1 or BRCA2. A recent article suggested that BRCA2-related EOC was associated with an improved prognosis, but the effect of BRCA1 remains unclear. OBJECTIVE To characterize the survival of BRCA carriers with EOC compared with noncarriers and to determine whether BRCA1 and BRCA2 carriers show similar survival patterns. DESIGN, SETTING, AND PARTICIPANTS A pooled analysis of 26 observational studies on the survival of women with ovarian cancer, which included data from 1213 EOC cases with pathogenic germline mutations in BRCA1 (n = 909) or BRCA2 (n = 304) and from 2666 noncarriers recruited and followed up at variable times between 1987 and 2010 (the median year of diagnosis was 1998). MAIN OUTCOME MEASURE Five-year overall mortality. RESULTS The 5-year overall survival was 36% (95% CI, 34%-38%) for noncarriers, 44% (95% CI, 40%-48%) for BRCA1 carriers, and 52% (95% CI, 46%-58%) for BRCA2 carriers. After adjusting for study and year of diagnosis, BRCA1 and BRCA2 mutation carriers showed a more favorable survival than noncarriers (for BRCA1: hazard ratio [HR], 0.78; 95% CI, 0.68-0.89; P < .001; and for BRCA2: HR, 0.61; 95% CI, 0.50-0.76; P < .001). These survival differences remained after additional adjustment for stage, grade, histology, and age at diagnosis (for BRCA1: HR, 0.73; 95% CI, 0.64-0.84; P < .001; and for BRCA2: HR, 0.49; 95% CI, 0.39-0.61; P < .001). The BRCA1 HR estimate was significantly different from the HR estimated in the adjusted model (P for heterogeneity = .003). CONCLUSION Among patients with invasive EOC, having a germline mutation in BRCA1 or BRCA2 was associated with improved 5-year overall survival. BRCA2 carriers had the best prognosis.
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Affiliation(s)
- Kelly L Bolton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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25
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Mavaddat N, Barrowdale D, Andrulis IL, Domchek SM, Eccles D, Nevanlinna H, Ramus SJ, Spurdle A, Robson M, Sherman M, Mulligan AM, Couch FJ, Engel C, McGuffog L, Healey S, Sinilnikova OM, Southey MC, Terry MB, Goldgar D, O'Malley F, John EM, Janavicius R, Tihomirova L, Hansen TVO, Nielsen FC, Osorio A, Stavropoulou A, Benítez J, Manoukian S, Peissel B, Barile M, Volorio S, Pasini B, Dolcetti R, Putignano AL, Ottini L, Radice P, Hamann U, Rashid MU, Hogervorst FB, Kriege M, van der Luijt RB, Peock S, Frost D, Evans DG, Brewer C, Walker L, Rogers MT, Side LE, Houghton C, Weaver J, Godwin AK, Schmutzler RK, Wappenschmidt B, Meindl A, Kast K, Arnold N, Niederacher D, Sutter C, Deissler H, Gadzicki D, Preisler-Adams S, Varon-Mateeva R, Schönbuchner I, Gevensleben H, Stoppa-Lyonnet D, Belotti M, Barjhoux L, Isaacs C, Peshkin BN, Caldes T, de la Hoya M, Cañadas C, Heikkinen T, Heikkilä P, Aittomäki K, Blanco I, Lazaro C, Brunet J, Agnarsson BA, Arason A, Barkardottir RB, Dumont M, Simard J, Montagna M, Agata S, D'Andrea E, Yan M, Fox S, Rebbeck TR, Rubinstein W, Tung N, Garber JE, Wang X, Fredericksen Z, Pankratz VS, Lindor NM, Szabo C, Offit K, Sakr R, Gaudet MM, Singer CF, Tea MK, Rappaport C, Mai PL, Greene MH, Sokolenko A, Imyanitov E, Toland AE, Senter L, Sweet K, Thomassen M, Gerdes AM, Kruse T, Caligo M, Aretini P, Rantala J, von Wachenfeld A, Henriksson K, Steele L, Neuhausen SL, Nussbaum R, Beattie M, Odunsi K, Sucheston L, Gayther SA, Nathanson K, Gross J, Walsh C, Karlan B, Chenevix-Trench G, Easton DF, Antoniou AC. Pathology of breast and ovarian cancers among BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Cancer Epidemiol Biomarkers Prev 2012; 21:134-47. [PMID: 22144499 PMCID: PMC3272407 DOI: 10.1158/1055-9965.epi-11-0775] [Citation(s) in RCA: 445] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Previously, small studies have found that BRCA1 and BRCA2 breast tumors differ in their pathology. Analysis of larger datasets of mutation carriers should allow further tumor characterization. METHODS We used data from 4,325 BRCA1 and 2,568 BRCA2 mutation carriers to analyze the pathology of invasive breast, ovarian, and contralateral breast cancers. RESULTS There was strong evidence that the proportion of estrogen receptor (ER)-negative breast tumors decreased with age at diagnosis among BRCA1 (P-trend = 1.2 × 10(-5)), but increased with age at diagnosis among BRCA2, carriers (P-trend = 6.8 × 10(-6)). The proportion of triple-negative tumors decreased with age at diagnosis in BRCA1 carriers but increased with age at diagnosis of BRCA2 carriers. In both BRCA1 and BRCA2 carriers, ER-negative tumors were of higher histologic grade than ER-positive tumors (grade 3 vs. grade 1; P = 1.2 × 10(-13) for BRCA1 and P = 0.001 for BRCA2). ER and progesterone receptor (PR) expression were independently associated with mutation carrier status [ER-positive odds ratio (OR) for BRCA2 = 9.4, 95% CI: 7.0-12.6 and PR-positive OR = 1.7, 95% CI: 1.3-2.3, under joint analysis]. Lobular tumors were more likely to be BRCA2-related (OR for BRCA2 = 3.3, 95% CI: 2.4-4.4; P = 4.4 × 10(-14)), and medullary tumors BRCA1-related (OR for BRCA2 = 0.25, 95% CI: 0.18-0.35; P = 2.3 × 10(-15)). ER-status of the first breast cancer was predictive of ER-status of asynchronous contralateral breast cancer (P = 0.0004 for BRCA1; P = 0.002 for BRCA2). There were no significant differences in ovarian cancer morphology between BRCA1 and BRCA2 carriers (serous: 67%; mucinous: 1%; endometrioid: 12%; clear-cell: 2%). CONCLUSIONS/IMPACT: Pathologic characteristics of BRCA1 and BRCA2 tumors may be useful for improving risk-prediction algorithms and informing clinical strategies for screening and prophylaxis.
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Affiliation(s)
- Nasim Mavaddat
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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26
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Maxwell CA, Benítez J, Gómez-Baldó L, Osorio A, Bonifaci N, Fernández-Ramires R, Costes SV, Guinó E, Chen H, Evans GJR, Mohan P, Català I, Petit A, Aguilar H, Villanueva A, Aytes A, Serra-Musach J, Rennert G, Lejbkowicz F, Peterlongo P, Manoukian S, Peissel B, Ripamonti CB, Bonanni B, Viel A, Allavena A, Bernard L, Radice P, Friedman E, Kaufman B, Laitman Y, Dubrovsky M, Milgrom R, Jakubowska A, Cybulski C, Gorski B, Jaworska K, Durda K, Sukiennicki G, Lubiński J, Shugart YY, Domchek SM, Letrero R, Weber BL, Hogervorst FBL, Rookus MA, Collee JM, Devilee P, Ligtenberg MJ, van der Luijt RB, Aalfs CM, Waisfisz Q, Wijnen J, van Roozendaal CEP, Easton DF, Peock S, Cook M, Oliver C, Frost D, Harrington P, Evans DG, Lalloo F, Eeles R, Izatt L, Chu C, Eccles D, Douglas F, Brewer C, Nevanlinna H, Heikkinen T, Couch FJ, Lindor NM, Wang X, Godwin AK, Caligo MA, Lombardi G, Loman N, Karlsson P, Ehrencrona H, von Wachenfeldt A, Bjork Barkardottir R, Hamann U, Rashid MU, Lasa A, Caldés T, Andrés R, Schmitt M, Assmann V, Stevens K, Offit K, Curado J, Tilgner H, Guigó R, Aiza G, Brunet J, Castellsagué J, Martrat G, Urruticoechea A, Blanco I, Tihomirova L, Goldgar DE, Buys S, John EM, Miron A, Southey M, Daly MB, Schmutzler RK, Wappenschmidt B, Meindl A, Arnold N, Deissler H, Varon-Mateeva R, Sutter C, Niederacher D, Imyamitov E, Sinilnikova OM, Stoppa-Lyonne D, Mazoyer S, Verny-Pierre C, Castera L, de Pauw A, Bignon YJ, Uhrhammer N, Peyrat JP, Vennin P, Fert Ferrer S, Collonge-Rame MA, Mortemousque I, Spurdle AB, Beesley J, Chen X, Healey S, Barcellos-Hoff MH, Vidal M, Gruber SB, Lázaro C, Capellá G, McGuffog L, Nathanson KL, Antoniou AC, Chenevix-Trench G, Fleisch MC, Moreno V, Pujana MA. Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol 2011; 9:e1001199. [PMID: 22110403 PMCID: PMC3217025 DOI: 10.1371/journal.pbio.1001199] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/10/2011] [Indexed: 12/24/2022] Open
Abstract
Differentiated mammary epithelium shows apicobasal polarity, and loss of tissue organization is an early hallmark of breast carcinogenesis. In BRCA1 mutation carriers, accumulation of stem and progenitor cells in normal breast tissue and increased risk of developing tumors of basal-like type suggest that BRCA1 regulates stem/progenitor cell proliferation and differentiation. However, the function of BRCA1 in this process and its link to carcinogenesis remain unknown. Here we depict a molecular mechanism involving BRCA1 and RHAMM that regulates apicobasal polarity and, when perturbed, may increase risk of breast cancer. Starting from complementary genetic analyses across families and populations, we identified common genetic variation at the low-penetrance susceptibility HMMR locus (encoding for RHAMM) that modifies breast cancer risk among BRCA1, but probably not BRCA2, mutation carriers: n = 7,584, weighted hazard ratio ((w)HR) = 1.09 (95% CI 1.02-1.16), p(trend) = 0.017; and n = 3,965, (w)HR = 1.04 (95% CI 0.94-1.16), p(trend) = 0.43; respectively. Subsequently, studies of MCF10A apicobasal polarization revealed a central role for BRCA1 and RHAMM, together with AURKA and TPX2, in essential reorganization of microtubules. Mechanistically, reorganization is facilitated by BRCA1 and impaired by AURKA, which is regulated by negative feedback involving RHAMM and TPX2. Taken together, our data provide fundamental insight into apicobasal polarization through BRCA1 function, which may explain the expanded cell subsets and characteristic tumor type accompanying BRCA1 mutation, while also linking this process to sporadic breast cancer through perturbation of HMMR/RHAMM.
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Affiliation(s)
- Christopher A. Maxwell
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Javier Benítez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Biomedical Research Centre Network for Rare Diseases, Spain
| | - Laia Gómez-Baldó
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
| | - Ana Osorio
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Biomedical Research Centre Network for Rare Diseases, Spain
| | - Núria Bonifaci
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Ricardo Fernández-Ramires
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Biomedical Research Centre Network for Rare Diseases, Spain
| | - Sylvain V. Costes
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Elisabet Guinó
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Helen Chen
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Gareth J. R. Evans
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Pooja Mohan
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Isabel Català
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Anna Petit
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Helena Aguilar
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Alvaro Aytes
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Jordi Serra-Musach
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Gad Rennert
- CHS National Cancer Control Center, Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Flavio Lejbkowicz
- CHS National Cancer Control Center, Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, and IFOM Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Carla B. Ripamonti
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, and IFOM Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Alessandra Viel
- Division of Experimental Oncology 1, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Anna Allavena
- Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, and Consortium for Genomics Technology (Cogentech), Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, and IFOM Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Bella Kaufman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Maya Dubrovsky
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Roni Milgrom
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Anna Jakubowska
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Cezary Cybulski
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Bohdan Gorski
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Durda
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Grzegorz Sukiennicki
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Yin Yao Shugart
- Unit of Statistical Genetics, Division of Intramural Research Program, National Institute of Mental Health, National Institute of Health, Bethesda, Maryland, United States of America
| | - Susan M. Domchek
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Richard Letrero
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Barbara L. Weber
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Frans B. L. Hogervorst
- Family Cancer Clinic, Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Matti A. Rookus
- Department of Epidemiology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - J. Margriet Collee
- Department of Clinical Genetics, Rotterdam Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter Devilee
- Department of Genetic Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Rob B. van der Luijt
- Department of Clinical Molecular Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Cora M. Aalfs
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, the Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Juul Wijnen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - HEBON
- Hereditary Breast and Ovarian Cancer Group, the Netherlands
| | - EMBRACE
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Susan Peock
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Margaret Cook
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Clare Oliver
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | | | - D. Gareth Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Fiona Lalloo
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Rosalind Eeles
- The Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, United Kingdom
| | - Louise Izatt
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Carol Chu
- Yorkshire Regional Genetics Service, St. James's Hospital, Leeds, United Kingdom
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Fiona Douglas
- Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, United Kingdom
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Tuomas Heikkinen
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noralane M. Lindor
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Maria A. Caligo
- Section of Genetic Oncology, Department of Oncology, University of Pisa, and Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Grazia Lombardi
- Section of Genetic Oncology, Department of Oncology, University of Pisa, and Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Niklas Loman
- Department of Oncology, Lund University Hospital, Lund, Sweden
| | - Per Karlsson
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hans Ehrencrona
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - SWE-BRCA
- Swedish Breast Cancer Study, Sweden
| | | | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Muhammad U. Rashid
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany, and Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Adriana Lasa
- Genetic Service, Hospital de la Santa Creu i Sant Pau, Barcelona, Catalonia, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Madrid, Spain
| | - Raquel Andrés
- Medical Oncology Division, Hospital Clínico de Zaragoza, Zaragoza, Spain
| | - Michael Schmitt
- Department of Internal Medicine III, University of Rostock, Rostock, Germany
| | - Volker Assmann
- Center for Experimental Medicine, Institute of Tumor Biology, University Hospital Hamburg–Eppendorf, Hamburg, Germany
| | - Kristen Stevens
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - João Curado
- Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG), Biomedical Research Park of Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Hagen Tilgner
- Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG), Biomedical Research Park of Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG), Biomedical Research Park of Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Gemma Aiza
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Joan Brunet
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Joan Castellsagué
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Griselda Martrat
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Ander Urruticoechea
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Ignacio Blanco
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | | | - David E. Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Saundra Buys
- Department of Internal Medicine, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Alexander Miron
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Melissa Southey
- Centre for Molecular, Environmental, Genetic and Analytic (MEGA) Epidemiology, Melbourne School of Population Health, The University of Melbourne, Victoria, Australia
| | - Mary B. Daly
- Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - BCFR
- Breast Cancer Family Registry, United States of America
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer and Center of Integrated Oncology, University of Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer and Center of Integrated Oncology, University of Cologne, Cologne, Germany
| | - Alfons Meindl
- Department of Obstetrics and Gynaecology, Klinikum rechts der Isar, Technical University, Munich, Germany
| | - Norbert Arnold
- Division of Oncology, Department of Gynaecology and Obstetrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Helmut Deissler
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | | | - Christian Sutter
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Dieter Niederacher
- Division of Molecular Genetics, Department of Gynaecology and Obstetrics, Clinical Center University of Düsseldorf, Düsseldorf, Germany
| | - Evgeny Imyamitov
- N. N. Petrov Institute of Oncology, Saint-Petersburg, Russian Federation
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Centre Hospitalier Universitaire de Lyon, Centre Léon Bérard, Lyon, France
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Dominique Stoppa-Lyonne
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Sylvie Mazoyer
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Carole Verny-Pierre
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Laurent Castera
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Antoine de Pauw
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Yves-Jean Bignon
- Département d'Oncogénétique, Centre Jean Perrin, Université de Clermont-Ferrand, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Département d'Oncogénétique, Centre Jean Perrin, Université de Clermont-Ferrand, Clermont-Ferrand, France
| | - Jean-Philippe Peyrat
- Laboratoire d'Oncologie Moléculaire Humaine, Centre Oscar Lambret, Lille, France
| | - Philippe Vennin
- Consultation d'Oncogénétique, Centre Oscar Lambret, Lille, France
| | - Sandra Fert Ferrer
- Laboratoire de Génétique Chromosomique, Hôtel Dieu Centre Hospitalier, Chambéry, France
| | - Marie-Agnès Collonge-Rame
- Service de Génétique-Histologie-Biologie du Développement et de la Reproduction, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | | | - GEMO Study Collaborators
- GEMO Study (Genetics Network “Groupe Génétique et Cancer”), Fédération Nationale des Centres de Lutte Contre le Cancer, France
| | | | | | - Xiaoqing Chen
- Queensland Institute of Medical Research, Brisbane, Australia
| | - Sue Healey
- Queensland Institute of Medical Research, Brisbane, Australia
| | - kConFab
- The Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer, Peter MacCallum Cancer Institute, East Melbourne, Australia
| | - Mary Helen Barcellos-Hoff
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen B. Gruber
- Department of Internal Medicine, Epidemiology, Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Conxi Lázaro
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Gabriel Capellá
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Katherine L. Nathanson
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | | | - Markus C. Fleisch
- Department of Obstetrics and Gynaecologie, Heinrich-Heine-University, Duesseldorf, Germany
| | - Víctor Moreno
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Miguel Angel Pujana
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
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Lu Y, Liu P, Van den Bergh F, Zellmer V, James M, Wen W, Grubbs CJ, Lubet RA, You M. Modulation of Gene Expression and Cell-Cycle Signaling Pathways by the EGFR Inhibitor Gefitinib (Iressa) in Rat Urinary Bladder Cancer. Cancer Prev Res (Phila) 2011; 5:248-59. [DOI: 10.1158/1940-6207.capr-10-0363] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Analysis of RB1 mRNA from blood leukocytes of patients with retinoblastoma identified the effects of mutations involving consensus splice site, exonic substitution and whole-exon deletions identified in genomic DNA of these patients. In addition, this study identified mutations in cases in which no mutations were detectable in the genomic DNA. One proband had mutation at the canonical splice site at +5 position of IVS22, and analysis of the transcripts in this family revealed skipping of exon 22 in three members of this family. In one proband, a missense substitution of c.652T greater than G (g.56897T greater than G; Leu218Val) in exon 7 led to splicing aberrations involving deletions of exons 7 and 8, suggesting the formation of a cryptic splice site. In two probands with no detectable changes in the genomic DNA upon screening of RB1 exons and flanking intronic sequences, transcripts were found to have deletions of exon 6 in one, and exons 21 and 22 in another family. In two probands, RNA analysis confirmed genomic deletions involving one or more exons. This study reveals novel effects of RB1 mutations on splicing and suggests the utility of RNA analysis as an adjunct to mutational screening of genomic DNA in retinoblastoma.
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Antoniou AC, Kartsonaki C, Sinilnikova OM, Soucy P, McGuffog L, Healey S, Lee A, Peterlongo P, Manoukian S, Peissel B, Zaffaroni D, Cattaneo E, Barile M, Pensotti V, Pasini B, Dolcetti R, Giannini G, Putignano AL, Varesco L, Radice P, Mai PL, Greene MH, Andrulis IL, Glendon G, Ozcelik H, Thomassen M, Gerdes AM, Kruse TA, Birk Jensen U, Crüger DG, Caligo MA, Laitman Y, Milgrom R, Kaufman B, Paluch-Shimon S, Friedman E, Loman N, Harbst K, Lindblom A, Arver B, Ehrencrona H, Melin B, Nathanson KL, Domchek SM, Rebbeck T, Jakubowska A, Lubinski J, Gronwald J, Huzarski T, Byrski T, Cybulski C, Gorski B, Osorio A, Ramón y Cajal T, Fostira F, Andrés R, Benitez J, Hamann U, Hogervorst FB, Rookus MA, Hooning MJ, Nelen MR, van der Luijt RB, van Os TAM, van Asperen CJ, Devilee P, Meijers-Heijboer HEJ, Gómez Garcia EB, Peock S, Cook M, Frost D, Platte R, Leyland J, Evans DG, Lalloo F, Eeles R, Izatt L, Adlard J, Davidson R, Eccles D, Ong KR, Cook J, Douglas F, Paterson J, Kennedy MJ, Miedzybrodzka Z, Godwin A, Stoppa-Lyonnet D, Buecher B, Belotti M, Tirapo C, Mazoyer S, Barjhoux L, Lasset C, Leroux D, Faivre L, Bronner M, Prieur F, Nogues C, Rouleau E, Pujol P, Coupier I, Frénay M, Hopper JL, Daly MB, Terry MB, John EM, Buys SS, Yassin Y, Miron A, Goldgar D, Singer CF, Tea MK, Pfeiler G, Dressler AC, Hansen TVO, Jønson L, Ejlertsen B, Barkardottir RB, Kirchhoff T, Offit K, Piedmonte M, Rodriguez G, Small L, Boggess J, Blank S, Basil J, Azodi M, Toland AE, Montagna M, Tognazzo S, Agata S, Imyanitov E, Janavicius R, Lazaro C, Blanco I, Pharoah PDP, Sucheston L, Karlan BY, Walsh CS, Olah E, Bozsik A, Teo SH, Seldon JL, Beattie MS, van Rensburg EJ, Sluiter MD, Diez O, Schmutzler RK, Wappenschmidt B, Engel C, Meindl A, Ruehl I, Varon-Mateeva R, Kast K, Deissler H, Niederacher D, Arnold N, Gadzicki D, Schönbuchner I, Caldes T, de la Hoya M, Nevanlinna H, Aittomäki K, Dumont M, Chiquette J, Tischkowitz M, Chen X, Beesley J, Spurdle AB, Neuhausen SL, Chun Ding Y, Fredericksen Z, Wang X, Pankratz VS, Couch F, Simard J, Easton DF, Chenevix-Trench G. Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers. Hum Mol Genet 2011; 20:3304-21. [PMID: 21593217 PMCID: PMC3652640 DOI: 10.1093/hmg/ddr226] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 05/09/2011] [Accepted: 05/16/2011] [Indexed: 11/15/2022] Open
Abstract
Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r(2) = 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 × 10(-9) for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 × 10(-8) for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women.
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Affiliation(s)
- Antonis C Antoniou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK.
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Ghigna C, Valacca C, Biamonti G. Alternative splicing and tumor progression. Curr Genomics 2011; 9:556-70. [PMID: 19516963 PMCID: PMC2694562 DOI: 10.2174/138920208786847971] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Revised: 08/12/2008] [Accepted: 08/18/2008] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing is a key molecular mechanism for increasing the functional diversity of the eukaryotic proteomes. A large body of experimental data implicates aberrant splicing in various human diseases, including cancer. Both mutations in cis-acting splicing elements and alterations in the expression and/or activity of splicing regulatory factors drastically affect the splicing profile of many cancer-associated genes. In addition, the splicing profile of several cancer-associated genes is altered in particular types of cancer arguing for a direct role of specific splicing isoforms in tumor progression. Deciphering the mechanisms underlying aberrant splicing in cancer may prove crucial to understand how splicing machinery is controlled and integrated with other cellular processes, in particular transcription and signaling pathways. Moreover, the characterization of splicing deregulation in cancer will lead to a better comprehension of malignant transformation. Cancer-associated alternative splicing variants may be new tools for the diagnosis and classification of cancers and could be the targets for innovative therapeutical interventions based on highly selective splicing correction approaches.
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Affiliation(s)
- Claudia Ghigna
- Istituto di Genetica Molecolare - Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207. 27100 Pavia, Italy
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Assessing the RNA effect of 26 DNA variants in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat 2011; 132:979-92. [PMID: 21735045 DOI: 10.1007/s10549-011-1661-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 06/24/2011] [Indexed: 12/17/2022]
Abstract
Comprehensive genetic testing of the breast cancer susceptibility genes BRCA1 and BRCA2 identified approximately 16% of variants of unknown significance (VUS), a significant proportion of which could affect the correct splicing of the genes. Our aim is to establish a workflow for classifying VUS in these complex genes, the first stage of which is splicing analysis. We used a combined approach consisting of five in silico splicing prediction programs and RT-PCR analysis for a set of 26 variants not previously studied at the mRNA level and six variants that had already been studied, four of which were used as positive controls as they were found to affect the splicing of these genes and the other two were used as negative controls. We identified a splicing defect in 8 of the 26 newly studied variants and ruled out splicing alteration in the remaining 18 variants. The results for the four positive and the two negative control variants were consistent with results presented in the literature. Our results strongly suggest that the combination of RNA analysis and in silico programs is an important step towards the classification of VUS. The results revealed a very high correlation between experimental data and in silico programs when using tools for predicting acceptor/donor sites but a lower correlation in the case of tools for identifying ESE elements.
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Raponi M, Kralovicova J, Copson E, Divina P, Eccles D, Johnson P, Baralle D, Vorechovsky I. Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6. Hum Mutat 2011; 32:436-44. [PMID: 21309043 DOI: 10.1002/humu.21458] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Accepted: 01/07/2011] [Indexed: 12/29/2022]
Abstract
Missense, nonsense, and translationally silent mutations can inactivate genes by altering the inclusion of mutant exons in mRNA, but their overall frequency among disease-causing exonic substitutions is unknown. Here, we have tested missense and silent mutations deposited in the BRCA1 mutation databases of unclassified variants for their effects on exon inclusion. Analysis of 21 BRCA1 variants using minigene assays revealed a single exon-skipping mutation c.231G>T. Comprehensive mutagenesis of an adjacent 12-nt segment showed that this silent mutation resulted in a higher level of exon skipping than the 35 other single-nucleotide substitutions. Exon inclusion levels of mutant constructs correlated significantly with predicted splicing enhancers/silencers, prompting the development of two online utilities freely available at http://www.dbass.org.uk. EX-SKIP quickly estimates which allele is more susceptible to exon skipping, whereas HOT-SKIP examines all possible mutations at each exon position and identifies candidate exon-skipping positions/substitutions. We demonstrate that the distribution of exon-skipping and disease-associated substitutions previously identified in coding regions was biased toward top-ranking HOT-SKIP mutations. Finally, we show that proteins 9G8, SC35, SF2/ASF, Tra2, and hnRNP A1 were associated with significant alterations of BRCA1 exon 6 inclusion in the mRNA. Together, these results facilitate prediction of exonic substitutions that reduce exon inclusion in mature transcripts.
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Affiliation(s)
- Michela Raponi
- University of Southampton School of Medicine, Southampton, United Kingdom
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Antoniou AC, Wang X, Fredericksen ZS, McGuffog L, Tarrell R, Sinilnikova OM, Healey S, Morrison J, Kartsonaki C, Lesnick T, Ghoussaini M, Barrowdale D, Peock S, Cook M, Oliver C, Frost D, Eccles D, Evans DG, Eeles R, Izatt L, Chu C, Douglas F, Paterson J, Stoppa-Lyonnet D, Houdayer C, Mazoyer S, Giraud S, Lasset C, Remenieras A, Caron O, Hardouin A, Berthet P, Hogervorst FBL, Rookus MA, Jager A, van den Ouweland A, Hoogerbrugge N, van der Luijt RB, Meijers-Heijboer H, Gómez García EB, Devilee P, Vreeswijk MPG, Lubinski J, Jakubowska A, Gronwald J, Huzarski T, Byrski T, Górski B, Cybulski C, Spurdle AB, Holland H, Goldgar DE, John EM, Hopper JL, Southey M, Buys SS, Daly MB, Terry MB, Schmutzler RK, Wappenschmidt B, Engel C, Meindl A, Preisler-Adams S, Arnold N, Niederacher D, Sutter C, Domchek SM, Nathanson KL, Rebbeck T, Blum JL, Piedmonte M, Rodriguez GC, Wakeley K, Boggess JF, Basil J, Blank SV, Friedman E, Kaufman B, Laitman Y, Milgrom R, Andrulis IL, Glendon G, Ozcelik H, Kirchhoff T, Vijai J, Gaudet MM, Altshuler D, Guiducci C, Loman N, Harbst K, Rantala J, Ehrencrona H, Gerdes AM, Thomassen M, Sunde L, Peterlongo P, Manoukian S, Bonanni B, Viel A, Radice P, Caldes T, de la Hoya M, Singer CF, Fink-Retter A, Greene MH, Mai PL, Loud JT, Guidugli L, Lindor NM, Hansen TVO, Nielsen FC, Blanco I, Lazaro C, Garber J, Ramus SJ, Gayther SA, Phelan C, Narod S, Szabo CI, Benitez J, Osorio A, Nevanlinna H, Heikkinen T, Caligo MA, Beattie MS, Hamann U, Godwin AK, Montagna M, Casella C, Neuhausen SL, Karlan BY, Tung N, Toland AE, Weitzel J, Olopade O, Simard J, Soucy P, Rubinstein WS, Arason A, Rennert G, Martin NG, Montgomery GW, Chang-Claude J, Flesch-Janys D, Brauch H, Severi G, Baglietto L, Cox A, Cross SS, Miron P, Gerty SM, Tapper W, Yannoukakos D, Fountzilas G, Fasching PA, Beckmann MW, Dos Santos Silva I, Peto J, Lambrechts D, Paridaens R, Rüdiger T, Försti A, Winqvist R, Pylkäs K, Diasio RB, Lee AM, Eckel-Passow J, Vachon C, Blows F, Driver K, Dunning A, Pharoah PPD, Offit K, Pankratz VS, Hakonarson H, Chenevix-Trench G, Easton DF, Couch FJ. A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor-negative breast cancer in the general population. Nat Genet 2010; 42:885-92. [PMID: 20852631 PMCID: PMC3130795 DOI: 10.1038/ng.669] [Citation(s) in RCA: 276] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 08/26/2010] [Indexed: 02/02/2023]
Abstract
Germline BRCA1 mutations predispose to breast cancer. To identify genetic modifiers of this risk, we performed a genome-wide association study in 1,193 individuals with BRCA1 mutations who were diagnosed with invasive breast cancer under age 40 and 1,190 BRCA1 carriers without breast cancer diagnosis over age 35. We took forward 96 SNPs for replication in another 5,986 BRCA1 carriers (2,974 individuals with breast cancer and 3,012 unaffected individuals). Five SNPs on 19p13 were associated with breast cancer risk (P(trend) = 2.3 × 10⁻⁹ to P(trend) = 3.9 × 10⁻⁷), two of which showed independent associations (rs8170, hazard ratio (HR) = 1.26, 95% CI 1.17-1.35; rs2363956 HR = 0.84, 95% CI 0.80-0.89). Genotyping these SNPs in 6,800 population-based breast cancer cases and 6,613 controls identified a similar association with estrogen receptor-negative breast cancer (rs2363956 per-allele odds ratio (OR) = 0.83, 95% CI 0.75-0.92, P(trend) = 0.0003) and an association with estrogen receptor-positive disease in the opposite direction (OR = 1.07, 95% CI 1.01-1.14, P(trend) = 0.016). The five SNPs were also associated with triple-negative breast cancer in a separate study of 2,301 triple-negative cases and 3,949 controls (P(trend) = 1 × 10⁻⁷) to P(trend) = 8 × 10⁻⁵; rs2363956 per-allele OR = 0.80, 95% CI 0.74-0.87, P(trend) = 1.1 × 10⁻⁷
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Affiliation(s)
- Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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Hastings ML, Berniac J, Liu YH, Abato P, Jodelka FM, Barthel L, Kumar S, Dudley C, Nelson M, Larson K, Edmonds J, Bowser T, Draper M, Higgins P, Krainer AR. Tetracyclines that promote SMN2 exon 7 splicing as therapeutics for spinal muscular atrophy. Sci Transl Med 2010; 1:5ra12. [PMID: 20161659 DOI: 10.1126/scitranslmed.3000208] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There is at present no cure or effective therapy for spinal muscular atrophy (SMA), a neurodegenerative disease that is the leading genetic cause of infant mortality. SMA usually results from loss of the SMN1 (survival of motor neuron 1) gene, which leads to selective motor neuron degeneration. SMN2 is nearly identical to SMN1 but has a nucleotide replacement that causes exon 7 skipping, resulting in a truncated, unstable version of the SMA protein. SMN2 is present in all SMA patients, and correcting SMN2 splicing is a promising approach for SMA therapy. We identified a tetracycline-like compound, PTK-SMA1, which stimulates exon 7 splicing and increases SMN protein levels in vitro and in vivo in mice. Unlike previously identified molecules that stimulate SMN production via SMN2 promoter activation or undefined mechanisms, PTK-SMA1 is a unique therapeutic candidate in that it acts by directly stimulating splicing of exon 7. Synthetic small-molecule compounds such as PTK-SMA1 offer an alternative to antisense oligonucleotide therapies that are being developed as therapeutics for a number of disease-associated splicing defects.
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Affiliation(s)
- Michelle L Hastings
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60044, USA.
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Woolfe A, Mullikin JC, Elnitski L. Genomic features defining exonic variants that modulate splicing. Genome Biol 2010; 11:R20. [PMID: 20158892 PMCID: PMC2872880 DOI: 10.1186/gb-2010-11-2-r20] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 02/03/2010] [Accepted: 02/16/2010] [Indexed: 12/21/2022] Open
Abstract
A comparative analysis of SNPs and their exonic and intronic environments identifies the features predictive of splice affecting variants. Background Single point mutations at both synonymous and non-synonymous positions within exons can have severe effects on gene function through disruption of splicing. Predicting these mutations in silico purely from the genomic sequence is difficult due to an incomplete understanding of the multiple factors that may be responsible. In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative. Results We assessed the features of single-nucleotide genomic variants verified to cause exon skipping and compared them to a large set of coding SNPs common in the human population, which are likely to have no effect on splicing. Our findings implicate a number of features important for their ability to discriminate splice-affecting variants, including the naturally occurring density of exonic splicing enhancers and exonic splicing silencers of the exon and intronic environment, extensive changes in the number of predicted exonic splicing enhancers and exonic splicing silencers, proximity to the splice junctions and evolutionary constraint of the region surrounding the variant. By extending this approach to additional datasets, we also identified relevant features of variants that cause increased exon inclusion and ectopic splice site activation. Conclusions We identified a number of features that have statistically significant representation among exonic variants that modulate splicing. These analyses highlight putative mechanisms responsible for splicing outcome and emphasize the role of features important for exon definition. We developed a web-tool, Skippy, to score coding variants for these relevant splice-modulating features.
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Affiliation(s)
- Adam Woolfe
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland 20892, USA.
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Moran-Jones K, Grindlay J, Jones M, Smith R, Norman JC. hnRNP A2 regulates alternative mRNA splicing of TP53INP2 to control invasive cell migration. Cancer Res 2010; 69:9219-27. [PMID: 19934309 DOI: 10.1158/0008-5472.can-09-1852] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Largely owing to widespread deployment of microarray analysis, many of the transcriptional events associated with invasive cell migration are becoming clear. However, the transcriptional drives to invasive migration are likely modified by alternative splicing of pre-mRNAs to produce functionally distinct patterns of protein expression. Heterogenous nuclear ribonucleoprotein (hnRNP A2) is a known regulator of alternative splicing that is upregulated in a number of invasive cancer types. Here, we report that although siRNA of hnRNP A2 had little influence on the ability of cells to migrate on plastic surfaces, the splicing regulator was clearly required for cells to move effectively on three-dimensional matrices and to invade into plugs of extracellular matrix proteins. We used exon-tiling microarrays to determine that hnRNP A2 controlled approximately six individual splicing events in a three-dimensional matrix-dependent fashion, one of which influenced invasive migration. Here, we show that alternative splicing of an exon in the 5' untranslated region of a gene termed TP53INP2 is a key event downstream of hnRNP A2 that is necessary for cells to invade the extracellular matrix. Furthermore, we report that the consequences of altered TP53INP2 splicing on invasion are likely mediated via alterations in Golgi complex integrity during migration on three-dimensional matrices.
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Affiliation(s)
- Kim Moran-Jones
- Beatson Institute for Cancer Research, Glasgow, United Kingdom
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A Case of Brooke-Spiegler Syndrome With a Novel Germline Deep Intronic Mutation in the CYLD Gene Leading to Intronic Exonization, Diverse Somatic Mutations, and Unusual Histology. Am J Dermatopathol 2009; 31:664-73. [DOI: 10.1097/dad.0b013e3181a05dad] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Analytical methods for inferring functional effects of single base pair substitutions in human cancers. Hum Genet 2009; 126:481-98. [PMID: 19434427 PMCID: PMC2762536 DOI: 10.1007/s00439-009-0677-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 04/29/2009] [Indexed: 02/08/2023]
Abstract
Cancer is a genetic disease that results from a variety of genomic alterations. Identification of some of these causal genetic events has enabled the development of targeted therapeutics and spurred efforts to discover the key genes that drive cancer formation. Rapidly improving sequencing and genotyping technology continues to generate increasingly large datasets that require analytical methods to identify functional alterations that deserve additional investigation. This review examines statistical and computational approaches for the identification of functional changes among sets of single-nucleotide substitutions. Frequency-based methods identify the most highly mutated genes in large-scale cancer sequencing efforts while bioinformatics approaches are effective for independent evaluation of both non-synonymous mutations and polymorphisms. We also review current knowledge and tools that can be utilized for analysis of alterations in non-protein-coding genomic sequence.
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Millevoi S, Bernat S, Telly D, Fouque F, Gladieff L, Favre G, Vagner S, Toulas C. The c.5242C>A BRCA1 missense variant induces exon skipping by increasing splicing repressors binding. Breast Cancer Res Treat 2009; 120:391-9. [PMID: 19404736 DOI: 10.1007/s10549-009-0392-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 03/28/2009] [Indexed: 02/02/2023]
Abstract
Several unclassified variants (UV) of BRCA1 can be deleterious by affecting normal pre-mRNA splicing. Here, we investigated the consequences at the mRNA level of the frequently encountered c.5242C>A UV in BRCA1 exon 18. We show that the c.5242C>A variant induces skipping of exon 18 in UV carriers and in vitro. This alteration predicted to disrupt the first BRCT domain of BRCA1. We show that two splicing repressors, hnRNP A1 and hnRNP H/F, display a significant preference toward binding with the mutated exon 18 and assemble into a protein complex. Sequence analysis of the region surrounding the c.5242C>A change reveals the presence of hnRNP A1 and hnRNP H/F binding sites, which are modified by several UVs. Mutation of these sites alters the RNA binding ability of both splicing regulators. In conclusion, our work supports the model of the pathogenicity of the c.5242C>A BRCA1 variant that induces exon skipping by creating a sequence with silencer properties. We propose that other UVs in exon 18 interfere with splicing complex assembly by perturbing the binding of hnRNP A1 and hnRNP H/F to their respective cis-elements. RNA analysis is therefore necessary for the assessment of the consequences of UVs on splicing of disease-associated genes and to enable adequate genetic counseling for breast/ovarian cancer families.
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Affiliation(s)
- Stefania Millevoi
- INSERM U563, Institut Claudius Regaud, 20-24 rue du Pont St Pierre, 31052, Toulouse, France.
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Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 2009; 37:e67. [PMID: 19339519 PMCID: PMC2685110 DOI: 10.1093/nar/gkp215] [Citation(s) in RCA: 1992] [Impact Index Per Article: 132.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Thousands of mutations are identified yearly. Although many directly affect protein expression, an increasing proportion of mutations is now believed to influence mRNA splicing. They mostly affect existing splice sites, but synonymous, non-synonymous or nonsense mutations can also create or disrupt splice sites or auxiliary cis-splicing sequences. To facilitate the analysis of the different mutations, we designed Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. It contains all available matrices for auxiliary sequence prediction as well as new ones for binding sites of the 9G8 and Tra2-β Serine-Arginine proteins and the hnRNP A1 ribonucleoprotein. We also developed new Position Weight Matrices to assess the strength of 5′ and 3′ splice sites and branch points. We evaluated HSF efficiency using a set of 83 intronic and 35 exonic mutations known to result in splicing defects. We showed that the mutation effect was correctly predicted in almost all cases. HSF could thus represent a valuable resource for research, diagnostic and therapeutic (e.g. therapeutic exon skipping) purposes as well as for global studies, such as the GEN2PHEN European Project or the Human Variome Project.
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DiFeo A, Martignetti JA, Narla G. The role of KLF6 and its splice variants in cancer therapy. Drug Resist Updat 2008; 12:1-7. [PMID: 19097929 DOI: 10.1016/j.drup.2008.11.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 11/03/2008] [Accepted: 11/04/2008] [Indexed: 12/21/2022]
Abstract
The Krüppel-like zinc finger transcription factor (KLF6) gene encodes a family of proteins generated through alternative splicing involved in the regulation of cancer development and progression. Alternative splicing of the KLF6 gene results in the production of at least four alternatively spliced isoforms, two of which are extensively discussed in this review. The full length form of the KLF6 gene is a tumor suppressor gene that is frequently inactivated by loss of heterozygozity (LOH), somatic mutation, and/or decreased expression in human cancer. While the exact mechanisms underlying KLF6's tumor suppressor roles are not completely known, a number of highly relevant, overlapping pathways have been described: transactivation of p21 in a p53-independent manner, reduction of cyclin D1/cdk4 complexes via interaction with cyclin D1, inhibition of c-Jun proto-oncoprotein activities, decreased VEGF expression, and induction of apoptosis. Kruppel-like factor 6 splice variant 1 (KLF6-SV1) is an oncogenic splice variant of the KLF6 tumor suppressor gene that is specifically overexpressed in a number of human cancers. Increased KLF6-SV1 expression is associated with poor prognosis in prostate, lung, and ovarian cancer. Furthermore, KLF6-SV1 has been shown to be biologically active, antagonizing the tumor suppressor function of KLF6 and promoting tumor growth and dissemination in both ovarian and prostate cancer models. In addition, a common germline polymorphism in the KLF6 gene associated with increased prostate cancer risk in a large multi-institutional study of 3411 men results in increased expression of KLF6-SV1. Furthermore, recent studies have demonstrated that targeted reduction of KLF6-SV1 results in the induction of spontaneous apoptosis in cell culture, synergizes with chemotherapeutic agents like cisplatin, and results in significant tumor regression in vivo. Combined, these data make the KLF6 gene family a compelling therapeutic target for both the treatment of localized as well as metastatic cancer.
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Affiliation(s)
- Analisa DiFeo
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
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Reyal F, van Vliet MH, Armstrong NJ, Horlings HM, de Visser KE, Kok M, Teschendorff AE, Mook S, van 't Veer L, Caldas C, Salmon RJ, van de Vijver MJ, Wessels LFA. A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the proliferation, immune response and RNA splicing modules in breast cancer. Breast Cancer Res 2008; 10:R93. [PMID: 19014521 PMCID: PMC2656909 DOI: 10.1186/bcr2192] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2008] [Revised: 07/31/2008] [Accepted: 11/13/2008] [Indexed: 01/28/2023] Open
Abstract
Introduction Several gene expression signatures have been proposed and demonstrated to be predictive of outcome in breast cancer. In the present article we address the following issues: Do these signatures perform similarly? Are there (common) molecular processes reported by these signatures? Can better prognostic predictors be constructed based on these identified molecular processes? Methods We performed a comprehensive analysis of the performance of nine gene expression signatures on seven different breast cancer datasets. To better characterize the functional processes associated with these signatures, we enlarged each signature by including all probes with a significant correlation to at least one of the genes in the original signature. The enrichment of functional groups was assessed using four ontology databases. Results The classification performance of the nine gene expression signatures is very similar in terms of assigning a sample to either a poor outcome group or a good outcome group. Nevertheless the concordance in classification at the sample level is low, with only 50% of the breast cancer samples classified in the same outcome group by all classifiers. The predictive accuracy decreases with the number of poor outcome assignments given to a sample. The best classification performance was obtained for the group of patients with only good outcome assignments. Enrichment analysis of the enlarged signatures revealed 11 functional modules with prognostic ability. The combination of the RNA-splicing and immune modules resulted in a classifier with high prognostic performance on an independent validation set. Conclusions The study revealed that the nine signatures perform similarly but exhibit a large degree of discordance in prognostic group assignment. Functional analyses indicate that proliferation is a common cellular process, but that other functional categories are also enriched and show independent prognostic ability. We provide new evidence of the potentially promising prognostic impact of immunity and RNA-splicing processes in breast cancer.
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Affiliation(s)
- Fabien Reyal
- Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Spurdle AB, Couch FJ, Hogervorst FBL, Radice P, Sinilnikova OM. Prediction and assessment of splicing alterations: implications for clinical testing. Hum Mutat 2008; 29:1304-13. [PMID: 18951448 PMCID: PMC2832470 DOI: 10.1002/humu.20901] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sequence variants that may result in splicing alterations are a particular class of inherited variants for which consequences can be more readily assessed, using a combination of bioinformatic prediction methods and in vitro assays. There is also a general agreement that a variant would invariably be considered pathogenic on the basis of convincing evidence that it results in transcript(s) carrying a premature stop codon or an in-frame deletion disrupting known functional domain(s). This commentary discusses current practices used to assess the clinical significance of this class of variants, provides suggestions to improve assessment, and highlights the issues involved in routine assessment of potential splicing aberrations. We conclude that classification of sequence variants that may alter splicing is greatly enhanced by supporting in vitro analysis. Additional studies that assess large numbers of variants for induction of splicing aberrations and exon skipping are needed to define the contribution of splicing/exon skipping to cancer and disease. These studies will also provide the impetus for development of algorithms that better predict splicing patterns. To facilitate variant classification and development of more specific bioinformatic tools, we call for the deposition of all laboratory data from splicing analyses into national and international databases.
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Affiliation(s)
- Amanda B Spurdle
- Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia.
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Anczuków O, Buisson M, Salles MJ, Triboulet S, Longy M, Lidereau R, Sinilnikova OM, Mazoyer S. Unclassified variants identified in BRCA1 exon 11: Consequences on splicing. Genes Chromosomes Cancer 2008; 47:418-26. [PMID: 18273839 DOI: 10.1002/gcc.20546] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Numerous mutations identified in breast/ovarian cancer families occur in splice sites of the BRCA1 gene. Splicing can also be disrupted by mutations occurring in exonic splicing enhancer (ESE) sequences. It is important to identify those mutations among the large number of nontruncating sequence variants that are identified during molecular diagnosis, as this could help to classify some of them as cancer predisposing. Several software programs have been designed to identify ESEs and can therefore be used to predict the outcome of genetic variation. However, it is not known whether these predictions are relevant in the case of BRCA1 exon 11 (3.4 kb). In this study, we assessed the consequences on splicing of 108 exon 11 variants identified in French breast/ovarian cancer families, most of them predicted to alter putative ESEs, and of nine variants located in the exon 11 alternative donor splice site. We employed a BRCA1 minigene consisting of exon 10 to 12, into which we introduced separately each of the variants to be tested. RNA was analyzed by RT-PCR after transient transfection of the resulting minigenes. None of the tested variants was found to dramatically alter splicing through disruption of an ESE. However, we identified several variants in the alternative donor splice site that are likely to be of biological significance as they appear to favor the expression of BRCA1-Delta11b over that of the full-length transcript. The results of this study will be of value to classify BRCA1 exon 11 variants of unknown significance. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
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Affiliation(s)
- Olga Anczuków
- Laboratoire de Génétique Moléculaire, Signalisation et Cancer UMR5201 CNRS, Lyon, France
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45
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Binding of DAZAP1 and hnRNPA1/A2 to an exonic splicing silencer in a natural BRCA1 exon 18 mutant. Mol Cell Biol 2008; 28:3850-60. [PMID: 18391021 DOI: 10.1128/mcb.02253-07] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A disease-causing G-to-T transversion at position +6 of BRCA1 exon 18 induces exclusion of the exon from the mRNA and, as has been suggested by in silico analysis, disrupts an ASF/SF2-dependent splicing enhancer. We show here using a pulldown assay with an internal standard that wild-type (WT) and mutant T6 sequences displayed similar ASF/SF2 binding efficiencies, which were significantly lower than that of a typical exonic splicing enhancer derived from the extra domain A exon of fibronectin. Overexpression or small interfering RNA (siRNA)-mediated depletion of ASF/SF2 did not affect the splicing of a WT BRCA1 minigene but resulted in an increase and decrease of T6 exon 18 inclusion, respectively. Furthermore, extensive mutation analysis using hybrid minigenes indicated that the T6 mutant creates a sequence with a prevalently inhibitory function. Indeed, RNA-protein interaction and siRNA experiments showed that the skipping of T6 BRCA1 exon 18 is due to the creation of a splicing factor-dependent silencer. This sequence specifically binds to the known repressor protein hnRNPA1/A2 and to DAZAP1, the involvement of which in splicing inhibition we have demonstrated. Our results indicate that the binding of the splicing factors hnRNPA1/A2 and DAZAP1 is the primary determinant of T6 BRCA1 exon 18 exclusion.
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46
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Ritchie W, Granjeaud S, Puthier D, Gautheret D. Entropy measures quantify global splicing disorders in cancer. PLoS Comput Biol 2008; 4:e1000011. [PMID: 18369415 PMCID: PMC2268240 DOI: 10.1371/journal.pcbi.1000011] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 01/28/2008] [Indexed: 11/19/2022] Open
Abstract
Most mammalian genes are able to express several splice variants in a phenomenon known as alternative splicing. Serious alterations of alternative splicing occur in cancer tissues, leading to expression of multiple aberrant splice forms. Most studies of alternative splicing defects have focused on the identification of cancer-specific splice variants as potential therapeutic targets. Here, we examine instead the bulk of non-specific transcript isoforms and analyze their level of disorder using a measure of uncertainty called Shannon's entropy. We compare isoform expression entropy in normal and cancer tissues from the same anatomical site for different classes of transcript variations: alternative splicing, polyadenylation, and transcription initiation. Whereas alternative initiation and polyadenylation show no significant gain or loss of entropy between normal and cancer tissues, alternative splicing shows highly significant entropy gains for 13 of the 27 cancers studied. This entropy gain is characterized by a flattening in the expression profile of normal isoforms and is correlated to the level of estimated cellular proliferation in the cancer tissue. Interestingly, the genes that present the highest entropy gain are enriched in splicing factors. We provide here the first quantitative estimate of splicing disruption in cancer. The expression of normal splice variants is widely and significantly disrupted in at least half of the cancers studied. We postulate that such splicing disorders may develop in part from splicing alteration in key splice factors, which in turn significantly impact multiple target genes.
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Affiliation(s)
- William Ritchie
- Université de la Méditerranée, INSERM ERM 206, Technologies Avancées pour le Génome et la Clinique, Marseille, France
| | - Samuel Granjeaud
- Université de la Méditerranée, INSERM ERM 206, Technologies Avancées pour le Génome et la Clinique, Marseille, France
| | - Denis Puthier
- Université de la Méditerranée, INSERM ERM 206, Technologies Avancées pour le Génome et la Clinique, Marseille, France
| | - Daniel Gautheret
- Université Paris-Sud 11, CNRS UMR 8621, Institut de Génétique et Microbiologie, Orsay, France
- * E-mail:
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Pando MP, Kotraiah V, McGowan K, Bracco L, Einstein R. Alternative isoform discrimination by the next generation of expression profiling microarrays. Expert Opin Ther Targets 2007; 10:613-25. [PMID: 16848696 DOI: 10.1517/14728222.10.4.613] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microarray expression profiling has revolutionised the way that many therapeutic targets have been identified over the past 10 years. High-density microarrays have allowed scientists to simultaneously scrutinise the expression of all genes encoded on a given genome. Although the data collected from classically designed microarrays greatly enriched the pool of information available to help guide the selection and design of new therapeutic strategies, they were unable to tell the complete story. The major limitation with most array designs is that they can only produce a global expression value for all transcripts produced from a specific locus and cannot monitor each individual alternative isoform produced from the interrogated locus. Recently, new array designs have been described, and become commercially available, that can efficiently monitor individual alternatively spliced isoforms produced from a single locus, allowing the research community to get a more accurate picture of the biological landscape of the expressed transcripts.
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Affiliation(s)
- Matthew P Pando
- ExonHit Therapeutics, Inc., 217 Perry Parkway, Bdg 5, Gaithersburg, MD 20877, USA
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Clancy JP, Rowe SM, Bebok Z, Aitken ML, Gibson R, Zeitlin P, Berclaz P, Moss R, Knowles MR, Oster RA, Mayer-Hamblett N, Ramsey B. No detectable improvements in cystic fibrosis transmembrane conductance regulator by nasal aminoglycosides in patients with cystic fibrosis with stop mutations. Am J Respir Cell Mol Biol 2007; 37:57-66. [PMID: 17347447 PMCID: PMC1899350 DOI: 10.1165/rcmb.2006-0173oc] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder caused by many types of genetic defects, including premature stop codons. Gentamicin can suppress stop mutations in CF transmembrane conductance regulator (CFTR) in vitro and in vivo, leading to improvements in CFTR-dependent ion transport and protein localization to the apical surface of respiratory epithelial cells. The primary objective of this study was to test whether nasally administered gentamicin or tobramycin could suppress premature stop mutations in CFTR, resulting in full-length, functional protein. A secondary objective was to obtain data to aid in the design of multicenter trials using the nasal potential difference as a study endpoint. A multicenter study was conducted in two cohorts of patients with CF, those heterozygous for stop mutations in the CFTR gene and those without nonsense mutations, to investigate the effects of both gentamicin and tobramycin administered over a 28-d period on sequential nasal potential difference and airway cell immunofluorescence endpoints. Eleven patients with CF with stop mutations were enrolled in a randomized, double-blinded, crossover fashion to receive each drug, while 18 subjects with CF without stop mutations were randomized 1:1 in a parallel fashion to receive one drug. After demonstration of drug delivery, neither aminoglycoside produced detectable changes in nasal ion transport or CFTR localization in brushed cells from either study group. These results with first-generation suppressive agents suggest the need for improved drug delivery methods and/or more potent suppressors of nonsense mutations to confer CFTR correction in subjects with CF heterozygous for nonsense mutations. The study provides valuable information on parameters of the nasal potential difference measurements for use in future multicenter clinical trials.
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Affiliation(s)
- John P Clancy
- Department of Pediatrics, University of Alabama at Birmingham, 1600 7th Avenue South, Birmingham, AL 35233, USA.
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Nielsen KB, Sørensen S, Cartegni L, Corydon TJ, Doktor TK, Schroeder LD, Reinert LS, Elpeleg O, Krainer AR, Gregersen N, Kjems J, Andresen BS. Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. Am J Hum Genet 2007; 80:416-32. [PMID: 17273963 PMCID: PMC1821120 DOI: 10.1086/511992] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 12/19/2006] [Indexed: 11/03/2022] Open
Abstract
The idea that point mutations in exons may affect splicing is intriguing and adds an additional layer of complexity when evaluating their possible effects. Even in the best-studied examples, the molecular mechanisms are not fully understood. Here, we use patient cells, model minigenes, and in vitro assays to show that a missense mutation in exon 5 of the medium-chain acyl-CoA dehydrogenase (MCAD) gene primarily causes exon skipping by inactivating a crucial exonic splicing enhancer (ESE), thus leading to loss of a functional protein and to MCAD deficiency. This ESE functions by antagonizing a juxtaposed exonic splicing silencer (ESS) and is necessary to define a suboptimal 3' splice site. Remarkably, a synonymous polymorphic variation in MCAD exon 5 inactivates the ESS, and, although this has no effect on splicing by itself, it makes splicing immune to deleterious mutations in the ESE. Furthermore, the region of MCAD exon 5 that harbors these elements is nearly identical to the exon 7 region of the survival of motor neuron (SMN) genes that contains the deleterious silent mutation in SMN2, indicating a very similar and finely tuned interplay between regulatory elements in these two genes. Our findings illustrate a mechanism for dramatic context-dependent effects of single-nucleotide polymorphisms on gene-expression regulation and show that it is essential that potential deleterious effects of mutations on splicing be evaluated in the context of the relevant haplotype.
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MESH Headings
- Acyl-CoA Dehydrogenase/genetics
- Cyclic AMP Response Element-Binding Protein/genetics
- Cyclic AMP Response Element-Binding Protein/metabolism
- DNA Primers/genetics
- Enhancer Elements, Genetic/genetics
- Exons/genetics
- Female
- Genes, BRCA1/physiology
- Humans
- Immunity
- Infant
- Infant, Newborn
- Lipid Metabolism, Inborn Errors/genetics
- Lipid Metabolism, Inborn Errors/immunology
- Molecular Sequence Data
- Muscular Atrophy, Spinal/genetics
- Muscular Atrophy, Spinal/immunology
- Mutation, Missense/genetics
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Polymorphism, Single Nucleotide
- RNA Splicing/genetics
- RNA Stability/genetics
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- SMN Complex Proteins
- Sequence Homology, Nucleic Acid
- Silencer Elements, Transcriptional/genetics
- Survival of Motor Neuron 2 Protein
- Transcription, Genetic
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Affiliation(s)
- Karsten Bork Nielsen
- Research Unit for Molecular Medicine, Aarhus University Hospital and Faculty of Health Science, Skejby Sygehus, Denmark
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Lovelock PK, Wong EM, Sprung CN, Marsh A, Hobson K, French JD, Southey M, Sculley T, Pandeya N, Brown MA, Chenevix-Trench G, Spurdle AB, McKay MJ. Prediction of BRCA1 and BRCA2 mutation status using post-irradiation assays of lymphoblastoid cell lines is compromised by inter-cell-line phenotypic variability. Breast Cancer Res Treat 2006; 104:257-66. [PMID: 17063265 DOI: 10.1007/s10549-006-9415-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2006] [Accepted: 09/20/2006] [Indexed: 01/09/2023]
Abstract
BACKGROUND AND PURPOSE Assays to determine the pathogenicity of unclassified sequence variants in disease-associated genes include the analysis of lymphoblastoid cell lines (LCLs). We assessed the ability of several assays of LCLs to distinguish carriers of germline BRCA1 and BRCA2 gene mutations from mutation-negative controls to determine their utility for use in a diagnostic setting. MATERIALS AND METHODS Post-ionising radiation cell viability and micronucleus formation, and telomere length were assayed in LCLs carrying BRCA1 or BRCA2 mutations, and in unaffected mutation-negative controls. RESULTS Post-irradiation cell viability and micronucleus induction assays of LCLs from individuals carrying pathogenic BRCA1 mutations, unclassified BRCA1 sequence variants or wildtype BRCA1 sequence showed significant phenotypic heterogeneity within each group. Responses were not consistent with predicted functional consequences of known pathogenic or normal sequences. Telomere length was also highly heterogeneous within groups of LCLs carrying pathogenic BRCA1 or BRCA2 mutations, and normal BRCA1 sequences, and was not predictive of mutation status. CONCLUSION Given the significant degree of phenotypic heterogeneity of LCLs after gamma-irradiation, and the lack of association with BRCA1 or BRCA2 mutation status, we conclude that the assays evaluated in this study should not be used as a means of differentiating pathogenic and non-pathogenic sequence variants for clinical application. We suggest that a range of normal controls must be included in any functional assays of LCLs to ensure that any observed differences between samples reflect the genotype under investigation rather than generic inter-individual variation.
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Affiliation(s)
- Paul K Lovelock
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
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