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Li D, Wan X, Yun Y, Li Y, Duan W. Genes Selectively Expressed in Rat Organs. Curr Genomics 2024; 25:261-297. [PMID: 39156728 PMCID: PMC11327808 DOI: 10.2174/0113892029273121240401060228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/24/2023] [Accepted: 12/05/2023] [Indexed: 08/20/2024] Open
Abstract
Background Understanding organic functions at a molecular level is important for scientists to unveil the disease mechanism and to develop diagnostic or therapeutic methods. Aims The present study tried to find genes selectively expressed in 11 rat organs, including the adrenal gland, brain, colon, duodenum, heart, ileum, kidney, liver, lung, spleen, and stomach. Materials and Methods Three normal male Sprague-Dawley (SD) rats were anesthetized, their organs mentioned above were harvested, and RNA in the fresh organs was extracted. Purified RNA was reversely transcribed and sequenced using the Solexa high-throughput sequencing technique. The abundance of a gene was measured by the expected value of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM). Genes in organs with the highest expression level were sought out and compared with their median value in organs. If a gene in the highest expressed organ was significantly different (p < 0.05) from that in the medianly expressed organ, accompanied by q value < 0.05, and accounted for more than 70% of the total abundance, the gene was assumed as the selective gene in the organ. Results & Discussion The Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) pathways were enriched by the highest expressed genes. Based on the criterion, 1,406 selective genes were screened out, 1,283 of which were described in the gene bank and 123 of which were waiting to be described. KEGG and GO pathways in the organs were partly confirmed by the known understandings and a good portion of the pathways needed further investigation. Conclusion The novel selective genes and organic functional pathways are useful for scientists to unveil the mechanisms of the organs at the molecular level, and the selective genes' products are candidate disease markers for organs.
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Affiliation(s)
- Dan Li
- The Department of Pharmacology, School of Basic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Xulian Wan
- School of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, 650500, China
| | - Yu Yun
- The Department of Pharmacology, School of Basic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yongkun Li
- School of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, 650500, China
| | - Weigang Duan
- School of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, 650500, China
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2
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de Traux De Wardin H, Cyrta J, Dermawan JK, Guillemot D, Orbach D, Aerts I, Pierron G, Antonescu CR. FGFR1 fusions as a novel molecular driver in rhabdomyosarcoma. Genes Chromosomes Cancer 2024; 63:e23232. [PMID: 38607246 PMCID: PMC11385681 DOI: 10.1002/gcc.23232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
The wide application of RNA sequencing in clinical practice has allowed the discovery of novel fusion genes, which have contributed to a refined molecular classification of rhabdomyosarcoma (RMS). Most fusions in RMS result in aberrant transcription factors, such as PAX3/7::FOXO1 in alveolar RMS (ARMS) and fusions involving VGLL2 or NCOA2 in infantile spindle cell RMS. However, recurrent fusions driving oncogenic kinase activation have not been reported in RMS. Triggered by an index case of an unclassified RMS (overlapping features between ARMS and sclerosing RMS) with a novel FGFR1::ANK1 fusion, we reviewed our molecular files for cases harboring FGFR1-related fusions. One additional case with an FGFR1::TACC1 fusion was identified in a tumor resembling embryonal RMS (ERMS) with anaplasia, but with no pathogenic variants in TP53 or DICER1 on germline testing. Both cases occurred in males, aged 7 and 24, and in the pelvis. The 2nd case also harbored additional alterations, including somatic TP53 and TET2 mutations. Two additional RMS cases (one unclassified, one ERMS) with FGFR1 overexpression but lacking FGFR1 fusions were identified by RNA sequencing. These two cases and the FGFR1::TACC1-positive case clustered together with the ERMS group by RNAseq. This is the first report of RMS harboring recurrent FGFR1 fusions. However, it remains unclear if FGFR1 fusions define a novel subset of RMS or alternatively, whether this alteration can sporadically drive the pathogenesis of known RMS subtypes, such as ERMS. Additional larger series with integrated genomic and epigenetic datasets are needed for better subclassification, as the resulting oncogenic kinase activation underscores the potential for targeted therapy.
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Affiliation(s)
- Henry de Traux De Wardin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pediatrics, Brussels University Hospital, Academic Children's Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Joanna Cyrta
- Department of Pathology, Institut Curie, PSL University, Paris, France
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
| | - Isabelle Aerts
- SIREDO Oncology Center (Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer), PSL University, Institut Curie, Paris, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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3
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Integrated genetic profiling of archival pediatric high-grade glial tumors and reassessment with 2021 WHO classification of paediatric CNS tumours. Cancer Genet 2023; 274-275:10-20. [PMID: 36917897 DOI: 10.1016/j.cancergen.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Though rare, pediatric high-grade gliomas (pHGG) are a leading cause of cancer-related mortality in children. We wanted to determine whether our currently available clinical laboratory methods could better define diagnosis for pHGG that had been archived at our institution for the past 20 years (1998 to 2017). We investigated 33 formalin-fixed paraffin-embedded pHGG using ThermoFisher Oncoscan SNP microarray with somatic mutation analysis, Sanger sequencing, and whole genome sequencing. These data were correlated with historical histopathological, chromosomal, clinical, and radiological data. Tumors were subsequently classified according to the 2021 WHO Classification of Paediatric CNS Tumours. All 33 tumors were found to have genetic aberrations that placed them within a 2021 WHO subtype and/or provided prognostic information; 6 tumors were upgraded from WHO CNS grade 3 to grade 4. New pHGG genetic features were found including two small cell glioblastomas with H3 G34 mutations not previously described; one tumor with STRN-NTRK2 fusion; and a congenital diffuse leptomeningeal glioneuronal tumor without a chromosomal 1p deletion but with KIAA1549-BRAF fusion. Overall, the combination of laboratory methods yielded key information for tumor classification. Thus, even small studies of these uncommon tumor types may yield new genetic features and possible new subtypes that warrant future investigations.
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4
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Guo S, Lin S. mRNA alternative polyadenylation (APA) in regulation of gene expression and diseases. Genes Dis 2021; 10:165-174. [PMID: 37013028 PMCID: PMC10066270 DOI: 10.1016/j.gendis.2021.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
The mRNA polyadenylation plays essential function in regulation of mRNA metabolism. Mis-regulations of mRNA polyadenylation are frequently linked with aberrant gene expression and disease progression. Under the action of polyadenylate polymerase, poly(A) tail is synthesized after the polyadenylation signal (PAS) sites on the mRNAs. Alternative polyadenylation (APA) often occurs in mRNAs with multiple poly(A) sites, producing different 3' ends for transcript variants, and therefore plays important functions in gene expression regulation. In this review, we first summarize the classical process of mRNA 3'-terminal formation and discuss the length control mechanisms of poly(A) in nucleus and cytoplasm. Then we review the research progress on alternative polyadenylation regulation and the APA site selection mechanism. Finally, we summarize the functional roles of APA in the regulation of gene expression and diseases including cancers.
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Affiliation(s)
- Siyao Guo
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
- Corresponding author. Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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5
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Qi Y, Chen S, Lu Y, Zhang Z, Wang S, Chen N, Shen M, Chen F, Chen M, Quan Y, Yang L, Xu Y, Su Y, Hu M, Wang J. Grape seed proanthocyanidin extract ameliorates ionizing radiation-induced hematopoietic stem progenitor cell injury by regulating Foxo1 in mice. Free Radic Biol Med 2021; 174:144-156. [PMID: 34389464 DOI: 10.1016/j.freeradbiomed.2021.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022]
Abstract
Ionizing radiation (IR)-induced excessive reactive oxygen species (ROS) is an important contributor of the injury of hematopoietic system. Grape seed proanthocyanidin extract (GSPE) is a new type of antioxidant, whereas whether it could ameliorate IR-induced hematopoietic injury remains unclear. Here, we show that GSPE treatment improves the survival of irradiated mice and alleviates IR-induced myelosuppression. Meanwhile, the hematopoietic reconstituting ability of hematopoietic stem cells (HSCs) in mice following irradiation exposure is significantly increased after GSPE treatment. Furthermore, GSPE treatment can reduce IR-induced ROS production and relieve DNA damage and apoptosis in hematopoietic stem progenitor cells (HSPCs). Interestingly, we find that a critical antioxidant-associated gene fokhead box transcription factor O1 (Foxo1) is significantly decreased in HSPCs after irradiation. Consistently, hematopoietic specific deletion of Foxo1 increases the radiosensitivity of mice. Further investigations reveal that GSPE treatment specifically upregulates the expression of Foxo1, as well as its target genes superoxide dismutase 1 (SOD1), superoxide dismutase 2 (SOD2) and catalase (CAT). Importantly, Foxo1 deficiency largely abolishes the radioprotection of GSPE on HSPCs. Collectively, our data demonstrate that GSPE plays an important role in ameliorating IR-induced HSPC injury via the Foxo1-mediated pathway. Therefore, GSPE may be used as a promising radioprotective agent.
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Affiliation(s)
- Yan Qi
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Shilei Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Yukai Lu
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Zihao Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Song Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Naicheng Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Mingqiang Shen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Fang Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Mo Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Yong Quan
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Lijing Yang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Yang Xu
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Yongping Su
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China
| | - Mengjia Hu
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China.
| | - Junping Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing, 400038, China.
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6
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Luo Y, Li Y, Ge P, Zhang K, Liu H, Jiang N. QKI-Regulated Alternative Splicing Events in Cervical Cancer: Pivotal Mechanism and Potential Therapeutic Strategy. DNA Cell Biol 2021; 40:1261-1277. [PMID: 34551268 DOI: 10.1089/dna.2021.0069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
QKI is a vital regulator in RNA splicing and maturation, but its role in cervical cancer (CC) is little known. In this study, we found that QKI is decreased in human CC, and overexpression of QKI inhibits HeLa cell proliferation and promotes the apoptosis of cancer cells. We identified hundreds of endogenous QKI-regulated alternative splicing events (ASEs) and differentially expressed genes (DEGs) in QKI-overexpressed HeLa cells by RNA-seq and selectively validated their expression by quantitative reverse-transcription polymerase chain reaction. The gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that QKI-regulated ASEs and DEGs were closely related to cancer, apoptosis, and transcriptional regulatory functions. In short, QKI may affect the occurrence and development of CC by regulating gene expression through AS.
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Affiliation(s)
- Yalan Luo
- Laboratory of Integrative Medicine, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Department of General Surgery, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Yuyuan Li
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Peng Ge
- Laboratory of Integrative Medicine, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Department of General Surgery, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Kaina Zhang
- Department of Gynecology and Obstetrics, Central Hospital of Zhuanghe City, Zhuanghe, China
| | - Huanhuan Liu
- Laboratory of Integrative Medicine, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Department of General Surgery, The First Affiliated Hospital, Dalian Medical University, Dalian, China.,Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Nan Jiang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital, Dalian Medical University, Dalian, China
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7
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Ida CM, Johnson DR, Nair AA, Davila J, Kollmeyer TM, Minn K, Fadra NM, Balcom JR, Fung KMA, Kim DK, Kaufmann TJ, Kipp BR, Halling KC, Jenkins RB, Giannini C. Polymorphous Low-Grade Neuroepithelial Tumor of the Young (PLNTY): Molecular Profiling Confirms Frequent MAPK Pathway Activation. J Neuropathol Exp Neurol 2021; 80:821-829. [PMID: 34363682 DOI: 10.1093/jnen/nlab075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polymorphous low-grade neuroepithelial tumor of the young (PLNTY) is a recently described epileptogenic tumor characterized by oligodendroglioma-like components, aberrant CD34 expression, and frequent mitogen-activated protein kinase (MAPK) pathway activation. We molecularly profiled 13 cases with diagnostic histopathological features of PLNTY (10 female; median age, 16 years; range, 5-52). Patients frequently presented with seizures (9 of 12 with available history) and temporal lobe tumors (9 of 13). MAPK pathway activating alterations were identified in all 13 cases. Fusions were present in the 7 youngest patients: FGFR2-CTNNA3 (n = 2), FGFR2-KIAA1598 (FGFR2-SHTN1) (n = 1), FGFR2-INA (n = 1), FGFR2-MPRIP (n = 1), QKI-NTRK2 (n = 1), and KIAA1549-BRAF (n = 1). BRAF V600E mutation was present in 6 patients (17 years or older). Two fusion-positive cases additionally harbored TP53/RB1 abnormalities suggesting biallelic inactivation. Copy number changes predominantly involving whole chromosomes were observed in all 10 evaluated cases, with losses of chromosome 10q occurring with FGFR2-KIAA1598 (SHTN1)/CTNNA3 fusions. The KIAA1549-BRAF and QKI-NTRK2 fusions were associated respectively with a 7q34 deletion and 9q21 duplication. This study shows that despite its name, PLNTY also occurs in older adults, who frequently show BRAF V600E mutation. It also expands the spectrum of the MAPK pathway activating alterations associated with PLNTY and demonstrates recurrent chromosomal copy number changes consistent with chromosomal instability.
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Affiliation(s)
- Cristiane M Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
| | - Derek R Johnson
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA (DRJ, DKK, TJK)
| | - Asha A Nair
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA (AAN, JD, NMF)
| | - Jaime Davila
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA (AAN, JD, NMF).,Department of Mathematics, Statistics and Computer Science, St Olaf College, Northfield, Minnesota, USA (JD)
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
| | - Kay Minn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
| | - Numrah M Fadra
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA (AAN, JD, NMF)
| | - Jessica R Balcom
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
| | - Kar-Ming A Fung
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA (KMAF)
| | - Dong Kun Kim
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA (DRJ, DKK, TJK)
| | - Timothy J Kaufmann
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA (DRJ, DKK, TJK)
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA (CMI, TMK, KM, JRB, BRK, KCH, RBJ, CG)
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8
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Baptiste M, Moinuddeen SS, Soliz CL, Ehsan H, Kaneko G. Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning. Genes (Basel) 2021; 12:722. [PMID: 34065872 PMCID: PMC8151328 DOI: 10.3390/genes12050722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022] Open
Abstract
Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person's variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e., precision oncology). Machine learning (ML), a subfield of artificial intelligence in which computers learn through experience, has a great potential to be used in precision oncology chiefly to help physicians make diagnostic decisions based on tumor images. A promising venue of ML in precision oncology is the integration of all available data from images to multi-omics big data for the holistic care of patients and high-risk healthy subjects. In this review, we provide a focused overview of precision oncology and ML with attention to breast cancer and glioma as well as the Bayesian networks that have the flexibility and the ability to work with incomplete information. We also introduce some state-of-the-art attempts to use and incorporate ML and genetic information in precision oncology.
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Affiliation(s)
| | | | | | | | - Gen Kaneko
- School of Arts & Sciences, University of Houston-Victoria, Victoria, TX 77901, USA; (M.B.); (S.S.M.); (C.L.S.); (H.E.)
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9
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Partial Response to Sorafenib in a Child With a Myeloid/Lymphoid Neoplasm, Eosinophilia, and a ZMYM2-FLT3 Fusion. J Pediatr Hematol Oncol 2021; 43:e508-e511. [PMID: 32852395 DOI: 10.1097/mph.0000000000001890] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/07/2020] [Indexed: 01/08/2023]
Abstract
Dysregulated tyrosine kinases in myeloid/lymphoid neoplasms with eosinophilia are rare, but do occur in children. To increase awareness of this diagnosis, we present a child who was diagnosed after a 3-year disease history. The patient was initially treated according to a T-cell lymphoblastic lymphoma protocol, but genetic analyses at recurrence revealed microdeletions resulting in an in-frame fusion of ZMYM2 and FLT3. Treatment with sorafenib, an FLT3 tyrosine kinase inhibitor, rapidly resulted in significant reduction of lymphadenopathy and normalization of white blood cell and eosinophil counts. At 17 months of treatment, he remains in complete hematologic, but not molecular remission.
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10
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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11
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Deland L, Keane S, Olsson Bontell T, Sjögren H, Fagman H, Øra I, De La Cuesta E, Tisell M, Nilsson JA, Ejeskär K, Sabel M, Abel F. Discovery of a rare GKAP1-NTRK2 fusion in a pediatric low-grade glioma, leading to targeted treatment with TRK-inhibitor larotrectinib. Cancer Biol Ther 2021; 22:184-195. [PMID: 33820494 PMCID: PMC8043191 DOI: 10.1080/15384047.2021.1899573] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Here we report a case of an 11-year-old girl with an inoperable tumor in the optic chiasm/hypothalamus, who experienced several tumor progressions despite three lines of chemotherapy treatment. Routine clinical examination classified the tumor as a BRAF-negative pilocytic astrocytoma. Copy-number variation profiling of fresh frozen tumor material identified two duplications in 9q21.32–33 leading to breakpoints within the GKAP1 and NTRK2 genes. RT-PCR Sanger sequencing revealed a GKAP1-NTRK2 exon 10–16 in-frame fusion, generating a putative fusion protein of 658 amino acids with a retained tyrosine kinase (TK) domain. Functional analysis by transient transfection of HEK293 cells showed the GKAP1-NTRK2 fusion protein to be activated through phosphorylation of the TK domain (Tyr705). Subsequently, downstream mediators of the MAPK- and PI3K-signaling pathways were upregulated in GKAP1-NTRK2 cells compared to NTRK2 wild-type; phosphorylated (p)ERK (3.6-fold), pAKT (1.8- fold), and pS6 ribosomal protein (1.4-fold). Following these findings, the patient was enrolled in a clinical trial and treated with the specific TRK-inhibitor larotrectinib, resulting in the arrest of tumor growth. The patient’s condition is currently stable and the quality of life has improved significantly. Our findings highlight the value of comprehensive clinical molecular screening of BRAF-negative pediatric low-grade gliomas, to reveal rare fusions serving as targets for precision therapy.
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Affiliation(s)
- Lily Deland
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Simon Keane
- Translational Medicine, School of Health Sciences, University of Skövde, Skövde, Sweden
| | - Thomas Olsson Bontell
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helene Sjögren
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Henrik Fagman
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ingrid Øra
- Department of Clinical Sciences, Lund University Hospital, Lund, Sweden.,HOPE/ITCC Phase I/II Trial Unit, Pediatric Oncology, Karolinska Hospital, Stockholm, Sweden
| | - Esther De La Cuesta
- Pharmaceuticals, Global Medical Affairs - Oncology, Bayer U.S., Whippany, USA
| | - Magnus Tisell
- Department of Clinical Neuroscience and Rehabilitation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Jonas A Nilsson
- Sahlgrenska Cancer Center, Department of Laboratory Medicine Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Katarina Ejeskär
- Translational Medicine, School of Health Sciences, University of Skövde, Skövde, Sweden
| | - Magnus Sabel
- Childhood Cancer Centre, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Frida Abel
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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12
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Gene Regulatory Network of ETS Domain Transcription Factors in Different Stages of Glioma. J Pers Med 2021; 11:jpm11020138. [PMID: 33671331 PMCID: PMC7922321 DOI: 10.3390/jpm11020138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/07/2021] [Accepted: 02/13/2021] [Indexed: 12/30/2022] Open
Abstract
The ETS domain family of transcription factors is involved in a number of biological processes, and is commonly misregulated in various forms of cancer. Using microarray datasets from patients with different grades of glioma, we have analyzed the expression profiles of various ETS genes, and have identified ETV1, ELK3, ETV4, ELF4, and ETV6 as novel biomarkers for the identification of different glioma grades. We have further analyzed the gene regulatory networks of ETS transcription factors and compared them to previous microarray studies, where Elk-1-VP16 or PEA3-VP16 were overexpressed in neuroblastoma cell lines, and we identify unique and common regulatory networks for these ETS proteins.
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13
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Al-Eitan LN, Al-Dalala IM, Elshammari AK, Khreisat WH, Nimiri AF, Alnaamneh AH, Aljamal HA, Alghamdi MA. Genetic Association of Epilepsy and Anti-Epileptic Drugs Treatment in Jordanian Patients. Pharmgenomics Pers Med 2020; 13:503-510. [PMID: 33116764 PMCID: PMC7584512 DOI: 10.2147/pgpm.s273125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022] Open
Abstract
Purpose The aim of this study was to investigate the possible effects of single-nucleotide polymorphisms (SNPs) within SLC1A1, SLC6A1, FAM131B, GPLD1, F2, GABRG2, GABRA1, and CACNG5 genes on response to anti-epileptic drugs (AEDs) and the genetic predisposition of epilepsy in Jordanian patients. Patients and Methods A total of 299 healthy individuals and 296 pediatric patients from the Jordanian population were recruited. Blood samples are collected, and genotyping was performed using a custom platform array analysis. Results The SLC1A1 rs10815018 and FAM131B rs4236482 polymorphisms found to be associated with epilepsy susceptibility. Moreover, SLC1A1 rs10815018 and GPLD1 rs1126617 polymorphisms were associated with generalized epilepsy (GE), while FAM131B rs4236482 is associated with the focal phenotype. Regarding the therapeutic response, the genetic polymorphisms of FAM131B rs4236482, GABRA1 rs2279020, and CACNG5 rs740805 are conferred poor response (resistance) to AEDs. There was no linkage of GLPD1 haplotypes to epilepsy, its subtypes, and treatment responsiveness. Conclusion Our findings suggested that SLC1A1, FAM131B, and GPLD1 polymorphisms increasing the risk of generating epilepsy, while FAM131B, GABRA1, and CACNG5 variants may play a role in predicting drug response in patients with epilepsy (PWE).
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Affiliation(s)
- Laith N Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, Jordan.,Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, Jordan
| | - Islam M Al-Dalala
- Department of Blood Banking, King Hussein Medical Centre, Royal Medical Services, Amman, Jordan
| | - Afrah K Elshammari
- Queen Rania Hospital for Children, King Hussein Medical Center, Royal Medical Services, Amman, Jordan
| | - Wael H Khreisat
- Queen Rania Hospital for Children, King Hussein Medical Center, Royal Medical Services, Amman, Jordan
| | - Aseel F Nimiri
- Queen Rania Hospital for Children, King Hussein Medical Center, Royal Medical Services, Amman, Jordan
| | - Adan H Alnaamneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Hanan A Aljamal
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Mansour A Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia.,Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
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14
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Abstract
Chordoma is a rare cancer in children and understanding the genesis of this tumor may contribute to treatment approaches. Evidence has proposed VDC/IE (vincristine, doxorubicin, cyclophosphamide/ifosfamide, etoposide) as a treatment option for young patients with chordoma to avoid the long-term effects of radiation therapy. We present a case of acute myeloid leukemia developing during treatment of localized chordoma of the clivus in a 20-month-old male. We propose a genomic relationship that may have contributed to the development of clival chordoma and acute myeloid leukemia without a latency period and advocate for genomic sequencing in children with chordoma before the initiation of systemic therapies.
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15
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Effects of the MAML2 genetic variants in glioma susceptibility and prognosis. Biosci Rep 2020; 39:220742. [PMID: 31652449 PMCID: PMC6822528 DOI: 10.1042/bsr20192091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/03/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Abnormal expression of the mastermind-like transcriptional co-activator 2 (MAML2) gene is oncogenic in several human cancers, including glioma. However, the relevance of MAML2 variants with glioma remains unknown. We aimed to investigate the role of MAML2 polymorphisms in glioma risk and prognosis among the Chinese Han population. METHODS Seven MAML2 single-nucleotide polymorphisms (SNPs) were genotyped using Agena MassARRAY system among 575 patients with glioma and 500 age- and gender-matched healthy controls. Logistic regression was used to estimate the association between MAML2 polymorphisms and glioma risk by calculating odds ratios (ORs) and 95% confidence intervals (CI). Kaplan-Meier survival analysis and univariate, multivariate Cox proportional hazard regression analyses for hazard ratios (HRs) and 95% CIs were performed to evaluate the contribution of MAML2 polymorphisms to glioma prognosis. RESULTS MAML2 rs7938889 and rs485842 polymorphisms were associated with the reduced risk of glioma (OR = 0.69, P=0.023; and OR = 0.81, P=0.032, respectively). Rs7115578 polymorphism had a lower susceptibility to glioma in males (OR = 0.68, P=0.034), while rs4598633 variant with a higher risk in females (OR = 1.66, P=0.016). Additionally, rs7115578 AG genotype represented a poorer prognosis of glioma (HR = 1.24, P=0.033) and astrocytoma (log-rank P=0.037, HR = 1.31, P=0.036). Furthermore, rs11021499 polymorphism had lower overall survival (OS) and progression-free survival (PFS) in patients with low-grade glioma. CONCLUSION We provided some novel data suggesting MAML2 polymorphisms might contribute to glioma risk and prognosis. Future studies are warranted to validate these findings and characterize mechanisms underlying these associations.
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16
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Novel CTNNB1-USP6 fusion in intravascular fasciitis of the large vein identified by next-generation sequencing. Virchows Arch 2020; 477:455-459. [PMID: 32170450 DOI: 10.1007/s00428-020-02792-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 02/05/2023]
Abstract
Intravascular fasciitis (IVF) is considered a rare variant of nodular fasciitis, which often involves small- and medium-sized blood vessels. Approximately 43 cases of IVF have been reported in the English literature to date. Here, we report an IVF case arising from the common iliac vein of the pelvic cavity in a 19-year-old Chinese man. Histologically, the lesion was confined within the vascular lumen and consisted of regular myofibroblasts immersed in a fibromyxoid stroma. The tumor cells showed a USP6 rearrangement by fluorescence in situ hybridization but were negative for MYH9-USP6 fusion by reverse transcription polymerase chain reaction. Subsequent next-generation sequencing identified the CTNNB1-USP6 fusion. To the best of our knowledge, the vessel involved in this case is the largest vein among the reported cases. The present case might be the first example of a USP6-rearranged lesion in this entity, suggesting that IVF should be included in the USP6-induced family.
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17
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Blessing MM, Blackburn PR, Krishnan C, Harrod VL, Barr Fritcher EG, Zysk CD, Jackson RA, Milosevic D, Nair AA, Davila JI, Balcom JR, Jenkins RB, Halling KC, Kipp BR, Nageswara Rao AA, Laack NN, Daniels DJ, Macon WR, Ida CM. Desmoplastic Infantile Ganglioglioma: A MAPK Pathway-Driven and Microglia/Macrophage-Rich Neuroepithelial Tumor. J Neuropathol Exp Neurol 2019; 78:1011-1021. [DOI: 10.1093/jnen/nlz086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
Abstract
MAPK pathway activation has been recurrently observed in desmoplastic infantile ganglioglioma/astrocytoma (DIG/DIA) with reported disproportionally low mutation allele frequencies relative to the apparent high tumor content, suggesting that MAPK pathway alterations may be subclonal. We sought to expand the number of molecularly profiled cases and investigate if tumor cell composition could account for the observed low mutation allele frequencies. Molecular (targeted neuro-oncology next-generation sequencing/RNA sequencing and OncoScan microarray) and immunohistochemical (CD68-PGM1/CD163/CD14/CD11c/lysozyme/CD3/CD20/CD34/PD-L1) studies were performed in 7 DIG. Activating MAPK pathway alterations were identified in 4 (57%) cases: 3 had a BRAF mutation (V600E/V600D/V600_W604delinsDQTDG, at 8%–27% variant allele frequency) and 1 showed a TPM3-NTRK1 fusion. Copy number changes were infrequent and nonrecurrent. All tumors had at least 30% of cells morphologically and immunophenotypically consistent with microglial/macrophage lineage. Two subtotally resected tumors regrew; 1 was re-excised and received adjuvant treatment (chemotherapy/targeted therapy), with clinical response to targeted therapy only. Even with residual tumor, all patients are alive (median follow-up, 83 months; 19–139). This study further supports DIG as another MAPK pathway-driven neuroepithelial tumor, thus expanding potential treatment options for tumors not amenable to surgical cure, and suggests that DIG is a microglia/macrophage-rich neuroepithelial tumor with frequent low driver mutation allele frequencies.
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Affiliation(s)
- Melissa M Blessing
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Patrick R Blackburn
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Chandra Krishnan
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Virginia L Harrod
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Emily G Barr Fritcher
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Christopher D Zysk
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Rory A Jackson
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Dragana Milosevic
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Asha A Nair
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Jaime I Davila
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Jessica R Balcom
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Robert B Jenkins
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Kevin C Halling
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Benjamin R Kipp
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Amulya A Nageswara Rao
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Nadia N Laack
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - David J Daniels
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - William R Macon
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
| | - Cristiane M Ida
- Departments of Laboratory Medicine and Pathology, Health Sciences Research, Pediatrics, Radiation Oncology, and Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and Departments of Pathology and Neuro-Oncology, Dell Children’s Medical Center, Austin, Texas
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18
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Berry NK, Scott RJ, Rowlings P, Enjeti AK. Clinical use of SNP-microarrays for the detection of genome-wide changes in haematological malignancies. Crit Rev Oncol Hematol 2019; 142:58-67. [PMID: 31377433 DOI: 10.1016/j.critrevonc.2019.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
Single nucleotide polymorphism (SNP) microarrays are commonly used for the clinical investigation of constitutional genomic disorders; however, their adoption for investigating somatic changes is being recognised. With increasing importance being placed on defining the cancer genome, a shift in technology is imperative at a clinical level. Microarray platforms have the potential to become frontline testing, replacing or complementing standard investigations such as FISH or karyotype. This 'molecular karyotype approach' exemplified by SNP-microarrays has distinct advantages in the investigation of several haematological malignancies. A growing body of literature, including guidelines, has shown support for the use of SNP-microarrays in the clinical laboratory to aid in a more accurate definition of the cancer genome. Understanding the benefits of this technology along with discussing the barriers to its implementation is necessary for the development and incorporation of SNP-microarrays in a clinical laboratory for the investigation of haematological malignancies.
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Affiliation(s)
- Nadine K Berry
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia.
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia
| | - Philip Rowlings
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
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19
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Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group. Cancer Genet 2018; 228-229:218-235. [DOI: 10.1016/j.cancergen.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/19/2022]
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