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Fontana D, Zambrotta GPM, Scannella A, Piazza R, Gambacorti-Passerini C. Late relapse of chronic myeloid leukemia after allogeneic bone marrow transplantation points to KANSARL (KANSL1::ARL17A) alteration: a case report with insights on the molecular landscape. Ann Hematol 2024; 103:1561-1568. [PMID: 38321229 PMCID: PMC11009776 DOI: 10.1007/s00277-024-05649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/31/2024] [Indexed: 02/08/2024]
Abstract
Chronic myeloid leukemia is a myeloproliferative neoplasm characterized by the presence of the Philadelphia chromosome and the consequent BCR::ABL1 oncoprotein. In the era before the introduction of tyrosine kinase inhibitors (TKIs), the only potentially curative treatment was allogeneic hematopoietic stem cell transplantation (HSCT). Here, we present the case of a patient affected by CML who experienced a relapse 20 years after allogeneic HSCT. Following relapse, the patient was treated with imatinib and bosutinib, resulting in a deep molecular response and successfully discontinued treatment. Additional analysis including whole-exome sequencing and RNA sequencing provided some insights on the molecular mechanisms of the relapse: the identification of the fusion transcript KANSL1::ARL17A (KANSARL), a cancer predisposition fusion gene, could justify a condition of genomic instability which may be associated with the onset and/or probably the late relapse of his CML.
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Affiliation(s)
- Diletta Fontana
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy.
| | - Giovanni Paolo Maria Zambrotta
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
- Hematology Division and Bone Marrow Unit, IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - Antonio Scannella
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
- Hematology Division and Bone Marrow Unit, IRCCS, San Gerardo dei Tintori, Monza, Italy
| | - Carlo Gambacorti-Passerini
- Department of Medicine and Surgery, University of Milano-Bicocca, via Cadore 48, Monza, MB, 20900, Italy
- Hematology Division and Bone Marrow Unit, IRCCS, San Gerardo dei Tintori, Monza, Italy
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2
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Monteuuis G, Schmitz U, Petrova V, Kearney PS, Rasko JEJ. Holding on to Junk Bonds: Intron Retention in Cancer and Therapy. Cancer Res 2020; 81:779-789. [PMID: 33046441 DOI: 10.1158/0008-5472.can-20-1943] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022]
Abstract
Intron retention (IR) in cancer was for a long time overlooked by the scientific community, as it was previously considered to be an artifact of a dysfunctional spliceosome. Technological advancements made in the last decade offer unique opportunities to explore the role of IR as a widespread phenomenon that contributes to the transcriptional diversity of many cancers. Numerous studies in cancer have shed light on dysregulation of cellular mechanisms that lead to aberrant and pathologic IR. IR is not merely a mechanism of gene regulation, but rather it can mediate cancer pathogenesis and therapeutic resistance in various human diseases. The burden of IR in cancer is governed by perturbations to mechanisms known to regulate this phenomenon and include epigenetic variation, mutations within the gene body, and splicing factor dysregulation. This review summarizes possible causes for aberrant IR and discusses the role of IR in therapy or as a consequence of disease treatment. As neoepitopes originating from retained introns can be presented on the cancer cell surface, the development of personalized cancer vaccines based on IR-derived neoepitopes should be considered. Ultimately, a deeper comprehension about the origins and consequences of aberrant IR may aid in the development of such personalized cancer vaccines.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Veronika Petrova
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia.,Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Sydney, Australia
| | - Padraic S Kearney
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Sydney, Australia. .,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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3
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Abstract
One of the mechanisms potentially explaining the discrepancy between the number of human genes and the functional complexity of organisms is generating alternative splice variants, an attribute of the vast majority of multi-exon genes. Members of the RAS family, such as NRAS, KRAS and HRAS, all of which are of significant importance in cancer biology, are no exception. The structural and functional differences of these splice variants, particularly if they contain the canonical (and therefore routinely targeted for diagnostic purposes) hot spot mutations, pose a significant challenge for targeted therapies. We must therefore consider whether these alternative splice variants constitute a minor component as originally thought and how therapies targeting the canonical isoforms affect these alternative splice variants and their overall functions.
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Affiliation(s)
- Erzsébet Rásó
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary.
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4
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Frankiw L, Baltimore D, Li G. Alternative mRNA splicing in cancer immunotherapy. Nat Rev Immunol 2019; 19:675-687. [PMID: 31363190 DOI: 10.1038/s41577-019-0195-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2019] [Indexed: 12/12/2022]
Abstract
Immunotherapies are yielding effective treatments for several previously untreatable cancers. Still, the identification of suitable antigens specific to the tumour that can be targets for cancer vaccines and T cell therapies is a challenge. Alternative processing of mRNA, a phenomenon that has been shown to alter the proteomic diversity of many cancers, may offer the potential of a broadened target space. Here, we discuss the promise of analysing mRNA processing events in cancer cells, with an emphasis on mRNA splicing, for the identification of potential new targets for cancer immunotherapy. Further, we highlight the challenges that must be overcome for this new avenue to have clinical applicability.
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Affiliation(s)
- Luke Frankiw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Guideng Li
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China. .,Suzhou Institute of Systems Medicine, Suzhou, China.
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5
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Rocca S, Carrà G, Poggio P, Morotti A, Brancaccio M. Targeting few to help hundreds: JAK, MAPK and ROCK pathways as druggable targets in atypical chronic myeloid leukemia. Mol Cancer 2018; 17:40. [PMID: 29455651 PMCID: PMC5817721 DOI: 10.1186/s12943-018-0774-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/01/2018] [Indexed: 12/19/2022] Open
Abstract
Atypical Chronic Myeloid Leukemia (aCML) is a myeloproliferative neoplasm characterized by neutrophilic leukocytosis and dysgranulopoiesis. From a genetic point of view, aCML shows a heterogeneous mutational landscape with mutations affecting signal transduction proteins but also broad genetic modifiers and chromatin remodelers, making difficult to understand the molecular mechanisms causing the onset of the disease. The JAK-STAT, MAPK and ROCK pathways are known to be responsible for myeloproliferation in physiological conditions and to be aberrantly activated in myeloproliferative diseases. Furthermore, experimental evidences suggest the efficacy of inhibitors targeting these pathways in repressing myeloproliferation, opening the way to deep clinical investigations. However, the activation status of these pathways is rarely analyzed when genetic mutations do not occur in a component of the signaling cascade. Given that mutations in functionally unrelated genes give rise to the same pathology, it is tempting to speculate that alteration in the few signaling pathways mentioned above might be a common feature of pathological myeloproliferation. If so, targeted therapy would be an option to be considered for aCML patients.
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Affiliation(s)
- Stefania Rocca
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126, Torino, Italy
| | - Giovanna Carrà
- Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Pietro Poggio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126, Torino, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, 10126, Torino, Italy.
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6
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Rocco P, Daniele R, Roberta S, Alessandra P, Luca DS, Pierangelo F, Vera M, Nicoletta C, Nitesh S, Carlo GP. OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes. Sci Rep 2017; 7:46290. [PMID: 28387367 PMCID: PMC5384236 DOI: 10.1038/srep46290] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 03/15/2017] [Indexed: 12/11/2022] Open
Abstract
The complicated, evolving landscape of cancer mutations poses a formidable challenge to identify cancer genes among the large lists of mutations typically generated in NGS experiments. The ability to prioritize these variants is therefore of paramount importance. To address this issue we developed OncoScore, a text-mining tool that ranks genes according to their association with cancer, based on available biomedical literature. Receiver operating characteristic curve and the area under the curve (AUC) metrics on manually curated datasets confirmed the excellent discriminating capability of OncoScore (OncoScore cut-off threshold = 21.09; AUC = 90.3%, 95% CI: 88.1-92.5%), indicating that OncoScore provides useful results in cases where an efficient prioritization of cancer-associated genes is needed.
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Affiliation(s)
- Piazza Rocco
- University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy
| | | | - Spinelli Roberta
- University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy
| | | | - De Sano Luca
- University of Milano-Bicocca, Dept. of Informatics, 20125, Milano
| | | | - Magistroni Vera
- University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy
| | - Cordani Nicoletta
- University of Milano-Bicocca, Dept. of Medicine and Surgery, Monza, 20900, Italy
| | - Sharma Nitesh
- University of New Mexico, Department of Pediatrics, Albuquerque., USA
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7
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Ahmadloo S, Talebi S, Miryounesi M, Pasalar P, Keramatipour M. Functional Analysis of A Novel Splicing Mutation in The Mutase Gene of Two Unrelated Pedigrees. CELL JOURNAL 2016; 18:397-404. [PMID: 27602322 PMCID: PMC5011328 DOI: 10.22074/cellj.2016.4568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 11/22/2015] [Indexed: 01/04/2023]
Abstract
Objective Methylmalonic acidura (MMA) is a rare autosomal recessive inborn error of
metabolism. In this study we present a novel nucleotide change in the mutase (MUT)
gene of two unrelated Iranian pedigrees and introduce the methods used for its functional
analysis.
Materials and Methods Two probands with definite diagnosis of MMA and a common
novel variant in the MUT were included in a descriptive study. Bioinformatic prediction of
the splicing variant was done with different prediction servers. Reverse transcriptionpolymerase
chain reaction (RT-PCR) was done for splicing analysis and the products were
analyzed by sequencing.
Results The included index patients showed elevated levels of propionylcarnitine (C3).
Urine organic acid analysis confirmed the diagnosis of MMA, and screening for mutations in the MUT revealed a novel C to G variation at the 3´ splice acceptor site in intron
12. In silico analysis suggested the change as a mutation in a conserved sequence. The
splicing analysis showed that the C to G nucleotide change at position -3 in the acceptor
splice site can lead to retention of the intron 12 sequence.
Conclusion This is the first report of a mutation at the position -3 in the MUT intron
12 (c.2125-3C>G). The results suggest that the identified variation can be associated
with the typical clinical manifestations of MMA.
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Affiliation(s)
- Somayeh Ahmadloo
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Miryounesi
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parvin Pasalar
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Keramatipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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8
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Lavrov AV, Chelysheva EY, Smirnikhina SA, Shukhov OA, Turkina AG, Adilgereeva EP, Kutsev SI. Frequent variations in cancer-related genes may play prognostic role in treatment of patients with chronic myeloid leukemia. BMC Genet 2016; 17 Suppl 1:14. [PMID: 26822197 PMCID: PMC4895599 DOI: 10.1186/s12863-015-0308-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Genome variability of host genome and cancer cells play critical role in diversity of response to existing therapies and overall success in treating oncological diseases. In chronic myeloid leukemia targeted therapy with tyrosine kinase inhibitors demonstrates high efficacy in most of the patients. However about 15 % of patients demonstrate primary resistance to standard therapy. Whole exome sequencing is a good tool for unbiased search of genetic variations important for prognosis of survival and therapy efficacy in many cancers. We apply this approach to CML patients with optimal response and failure of tyrosine kinase therapy. RESULTS We analyzed exome variations between optimal responders and failures and found 7 variants in cancer-related genes with different genotypes in two groups of patients. Five of them were found in optimal responders: rs11579366, rs1990236, rs176037, rs10653661, rs3803264 and two in failures: rs3099950, rs9471966. These variants were found in genes associated with cancers (ANKRD35, DNAH9, MAGEC1, TOX3) or participating in cancer-related signaling pathways (THSD1, MORN2, PTCRA). CONCLUSION We found gene variants which may become early predictors of the therapy outcome and allow development of new early prognostic tests for estimation of therapy efficacy in CML patients. Normal genetic variation may influence therapy efficacy during targeted treatment of cancers.
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Affiliation(s)
- Alexander V Lavrov
- Laboratory of Mutagenesis, Federal State Budgetary Institution "Research Centre for Medical Genetics", Moskvorechie, 1, Moscow, 115478, Russia. .,Department of Molecular and Cellular Genetics, State Budgetary Educational Institution of Higher Professional Education "Russian National Research Medical University named after N.I. Pirogov" of Ministry of Health of the Russian Federation, Moscow, Russia.
| | - Ekaterina Y Chelysheva
- Scientific and Advisory Department of Chemotherapy of Myeloproliferative Disorders, Federal State-Funded Institution National Research Center for Hematology of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Svetlana A Smirnikhina
- Laboratory of Mutagenesis, Federal State Budgetary Institution "Research Centre for Medical Genetics", Moskvorechie, 1, Moscow, 115478, Russia
| | - Oleg A Shukhov
- Scientific and Advisory Department of Chemotherapy of Myeloproliferative Disorders, Federal State-Funded Institution National Research Center for Hematology of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Anna G Turkina
- Scientific and Advisory Department of Chemotherapy of Myeloproliferative Disorders, Federal State-Funded Institution National Research Center for Hematology of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Elmira P Adilgereeva
- Laboratory of Mutagenesis, Federal State Budgetary Institution "Research Centre for Medical Genetics", Moskvorechie, 1, Moscow, 115478, Russia
| | - Sergey I Kutsev
- Laboratory of Mutagenesis, Federal State Budgetary Institution "Research Centre for Medical Genetics", Moskvorechie, 1, Moscow, 115478, Russia.,Department of Molecular and Cellular Genetics, State Budgetary Educational Institution of Higher Professional Education "Russian National Research Medical University named after N.I. Pirogov" of Ministry of Health of the Russian Federation, Moscow, Russia
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9
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Jung H, Lee D, Lee J, Park D, Kim YJ, Park WY, Hong D, Park PJ, Lee E. Intron retention is a widespread mechanism of tumor-suppressor inactivation. Nat Genet 2015; 47:1242-8. [PMID: 26437032 DOI: 10.1038/ng.3414] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 09/08/2015] [Indexed: 12/14/2022]
Abstract
A substantial fraction of disease-causing mutations are pathogenic through aberrant splicing. Although genome profiling studies have identified somatic single-nucleotide variants (SNVs) in cancer, the extent to which these variants trigger abnormal splicing has not been systematically examined. Here we analyzed RNA sequencing and exome data from 1,812 patients with cancer and identified ∼900 somatic exonic SNVs that disrupt splicing. At least 163 SNVs, including 31 synonymous ones, were shown to cause intron retention or exon skipping in an allele-specific manner, with ∼70% of the SNVs occurring on the last base of exons. Notably, SNVs causing intron retention were enriched in tumor suppressors, and 97% of these SNVs generated a premature termination codon, leading to loss of function through nonsense-mediated decay or truncated protein. We also characterized the genomic features predictive of such splicing defects. Overall, this work demonstrates that intron retention is a common mechanism of tumor-suppressor inactivation.
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Affiliation(s)
- Hyunchul Jung
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Donghoon Lee
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Jongkeun Lee
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Cancer Immunology Branch, Division of Cancer Biology, National Cancer Center, Gyeonggi-do, South Korea
| | - Donghyun Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology, Samsung Electronics Company, Ltd., Seoul, South Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology, Samsung Electronics Company, Ltd., Seoul, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Dongwan Hong
- Research Institute, National Cancer Center, Gyeonggi-do, South Korea.,Cancer Immunology Branch, Division of Cancer Biology, National Cancer Center, Gyeonggi-do, South Korea
| | - Peter J Park
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Eunjung Lee
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
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10
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Adamia S, Kriangkum J, Belch AR, Pilarski LM. Aberrant posttranscriptional processing of hyaluronan synthase 1 in malignant transformation and tumor progression. Adv Cancer Res 2015; 123:67-94. [PMID: 25081526 DOI: 10.1016/b978-0-12-800092-2.00003-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
It is becoming increasingly apparent that splicing defects play a key role in cancer, and that alterations in genomic splicing elements promote aberrant splicing. Alternative splicing increases the diversity of the human transcriptome and increases the numbers of functional gene products. However, dysregulation that leads to aberrant pre-mRNA splicing can contribute to cancer. Hyaluronan (HA), known to be an important component of cancer progression, is synthesized by hyaluronan synthases (HASs). In cancer cells, hyaluronan synthase 1 (HAS1) pre-mRNA is abnormally spliced to generate a family of aberrant splice variants (HAS1Vs) that synthesize extracellular and intracellular HA. HAS1Vs are clinically relevant, being found almost exclusively in malignant cells. Expression of aberrant HAS1Vs predicts poor survival in multiple myeloma. In this review, we summarize the unusual properties of HAS1Vs and their relationship to cancer. HAS1Vs form heterogeneous multimers with normally spliced HAS1 as well as with each other and with HAS3. Aberrant variants of HAS1 synthesize HA. Extracellular HA synthesized by HAS1Vs is likely to promote malignant spread. We speculate that synthesis of intracellular HA plays a fundamental and early role in oncogenesis by promoting genetic instability and the emergence of viable cancer variants that lead to aggressive disease.
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Affiliation(s)
- Sophia Adamia
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
| | - Jitra Kriangkum
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Andrew R Belch
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
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11
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Jian X, Boerwinkle E, Liu X. In silico prediction of splice-altering single nucleotide variants in the human genome. Nucleic Acids Res 2014; 42:13534-44. [PMID: 25416802 PMCID: PMC4267638 DOI: 10.1093/nar/gku1206] [Citation(s) in RCA: 334] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/12/2014] [Accepted: 11/04/2014] [Indexed: 01/17/2023] Open
Abstract
In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies.
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Affiliation(s)
- Xueqiu Jian
- Division of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Human Genetics, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Division of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Human Genetics, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoming Liu
- Division of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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