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Camargo-Forero N, Orozco-Arias S, Perez Agudelo JM, Guyot R. HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Arch Virol 2023; 168:125. [PMID: 36988711 DOI: 10.1007/s00705-023-05747-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 02/03/2023] [Indexed: 03/30/2023]
Abstract
Human endogenous retroviruses (HERVs) are LTR retrotransposons that are present in the human genome. Among them, members of the HERV-K (HML-2) group are suspected to play a role in the development of different types of cancer, including lung, ovarian, and prostate cancer, as well as leukemia. Acute myeloid leukemia (AML) is an important disease that causes 1% of cancer deaths in the United States and has a survival rate of 28.7%. Here, we describe a method for assessing the statistical association between HERV-K (HML-2) transposable element insertion polymorphisms (or TIPs) and AML, using whole-genome sequencing and read mapping using TIP_finder software. Our results suggest that 101 polymorphisms involving HERV-K (HML-2) elements were correlated with AML, with a percentage between 44.4 to 56.6%, most of which (70) were located in the region from 8q24.13 to 8q24.21. Moreover, it was found that the TRIB1, LRATD2, POU5F1B, MYC, PCAT1, PVT1, and CCDC26 genes could be displaced or fragmented by TIPs. Furthermore, a general method was devised to facilitate analysis of the correlation between transposable element insertions and specific diseases. Finally, although the relationship between HERV-K (HML-2) TIPs and AML remains unclear, the data reported in this study indicate a statistical correlation, as supported by the χ2 test with p-values < 0.05.
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Affiliation(s)
- Nicolás Camargo-Forero
- School of Biology, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia.
- Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia.
| | | | - Romain Guyot
- UMR DIADE, Université de Montpellier, Institut de recherche pour le développement, CIRAD, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
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Sharma A, Blériot C, Currenti J, Ginhoux F. Oncofetal reprogramming in tumour development and progression. Nat Rev Cancer 2022; 22:593-602. [PMID: 35999292 DOI: 10.1038/s41568-022-00497-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 12/12/2022]
Abstract
Embryonic development is characterized by rapidly dividing cells, cellular plasticity and a highly vascular microenvironment. These features are similar to those of tumour tissue, in that malignant cells are characterized by their ability to proliferate and exhibit cellular plasticity. The tumour microenvironment also often includes immunosuppressive features. Reciprocal communication between various cellular subpopulations enables fetal and tumour tissues to proliferate, migrate and escape immune responses. Fetal-like reprogramming has been demonstrated in the tumour microenvironment, indicating extraordinary cellular plasticity and bringing an additional layer of cellular heterogeneity. More importantly, some of these features are also present during inflammation. This Perspective discusses the similarity between embryogenesis, inflammation and tumorigenesis, and describes the mechanisms of oncofetal reprogramming that enable tumour cells to escape from immune responses, promoting tumour growth and metastasis.
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Affiliation(s)
- Ankur Sharma
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia.
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia.
- Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | | | - Jennifer Currenti
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Florent Ginhoux
- INSERM U1015, Institut Gustave Roussy, Villejuif, France.
- Singapore Immunology Network, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore.
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.
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Gu Y, Lin X, Kapoor A, Chow MJ, Jiang Y, Zhao K, Tang D. The Oncogenic Potential of the Centromeric Border Protein FAM84B of the 8q24.21 Gene Desert. Genes (Basel) 2020; 11:genes11030312. [PMID: 32183428 PMCID: PMC7140883 DOI: 10.3390/genes11030312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
FAM84B is a risk gene in breast and prostate cancers. Its upregulation is associated with poor prognosis of prostate cancer, breast cancer, and esophageal squamous cell carcinoma. FAM84B facilitates cancer cell proliferation and invasion in vitro, and xenograft growth in vivo. The FAM84B and Myc genes border a 1.2 Mb gene desert at 8q24.21. Co-amplification of both occurs in 20 cancer types. Mice deficient of a 430 Kb fragment within the 1.2 Mb gene desert have downregulated FAM84B and Myc expressions concurrent with reduced breast cancer growth. Intriguingly, Myc works in partnership with other oncogenes, including Ras. FAM84B shares similarities with the H-Ras-like suppressor (HRASLS) family over their typical LRAT (lecithin:retinal acyltransferase) domain. This domain contains a catalytic triad, H23, H35, and C113, which constitutes the phospholipase A1/2 and O-acyltransferase activities of HRASLS1-5. These enzymatic activities underlie their suppression of Ras. FAM84B conserves H23 and H35 but not C113 with both histidine residues residing within a highly conserved motif that FAM84B shares with HRASLS1-5. Deletion of this motif abolishes FAM84B oncogenic activities. These properties suggest a collaboration of FAM84B with Myc, consistent with the role of the gene desert in strengthening Myc functions. Here, we will discuss recent research on FAM84B-derived oncogenic potential.
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Affiliation(s)
- Yan Gu
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Xiaozeng Lin
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Mathilda Jing Chow
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yanzhi Jiang
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Kuncheng Zhao
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Damu Tang
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- Correspondence: ; Tel.: +(905)-522-1155 (ext. 35168)
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Miller LH, Park SI, Saxe D, Lew G, Raikar SS. Clonal Evolution of B-Cell Acute Lymphoblastic Leukemia with del(9)(p13p21) into Mixed Phenotype Acute Leukemia Presenting as an Isolated Testicular Relapse. REPORTS 2019; 2:18. [PMID: 38370916 PMCID: PMC10873150 DOI: 10.3390/reports2030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Lineage switch in acute leukemias is a well-reported occurrence; however, most of these cases involve a switch from either lymphoid to myeloid or myeloid to lymphoid lineage. Here, we report a case of a 14-year-old male with B-cell acute lymphoblastic leukemia (B-ALL) who initially responded well to standard chemotherapy but then later developed mixed phenotype acute leukemia (MPAL) at relapse, likely reflecting a clonal evolution of the original leukemia with a partial phenotypic shift. The patient had a del(9)(p13p21) in his leukemia blasts at diagnosis, and the deletion persisted at relapse along with multiple additional cytogenetic aberrations. Interestingly, the patient presented with an isolated testicular lesion at relapse, which on further analysis revealed both a lymphoid and myeloid component. Unfortunately, the patient did not respond well to treatment at relapse and eventually succumbed to his disease. To our knowledge, an isolated extramedullary MPAL at relapse in a patient with previously diagnosed B-ALL has not been reported in the literature before.
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Affiliation(s)
- Lane H. Miller
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory University, Atlanta, GA 30322, USA
- Cancer and Blood Disorders Center, Children’s Minnesota, Minneapolis, MN 55404, USA
| | - Sunita I. Park
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Debra Saxe
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Glen Lew
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory University, Atlanta, GA 30322, USA
| | - Sunil S. Raikar
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory University, Atlanta, GA 30322, USA
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Fanoni D, Corti L, Alberti-Violetti S, Tensen CP, Venegoni L, Vermeer M, Willemze R, Berti E. Array-based CGH of primary cutaneous CD8+ aggressive EPIDERMO-tropic cytotoxic T-cell lymphoma. Genes Chromosomes Cancer 2018; 57:622-629. [DOI: 10.1002/gcc.22673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Daniele Fanoni
- Dipartimento di Fisiopatologia medico-chirurgica e dei trapianti; Universitá degli Studi di Milano; Milan Italy
| | - Laura Corti
- Department of Dermatology; Fondazione IRCCS Ca’ Granda - Ospedale Maggiore Policlinico; Milan Italy
| | - Silvia Alberti-Violetti
- Department of Dermatology; Fondazione IRCCS Ca’ Granda - Ospedale Maggiore Policlinico; Milan Italy
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale; Universitá degli Studi di Milano; Milan Italy
| | - Cornelis P. Tensen
- Department of Dermatology; Leiden University Medical Centre (LUMC); Leiden The Netherlands
| | - Luigia Venegoni
- Dipartimento di Fisiopatologia medico-chirurgica e dei trapianti; Universitá degli Studi di Milano; Milan Italy
| | - Maarten Vermeer
- Department of Dermatology; Leiden University Medical Centre (LUMC); Leiden The Netherlands
| | - Rein Willemze
- Department of Dermatology; Leiden University Medical Centre (LUMC); Leiden The Netherlands
| | - Emilio Berti
- Dipartimento di Fisiopatologia medico-chirurgica e dei trapianti; Universitá degli Studi di Milano; Milan Italy
- Department of Dermatology; Fondazione IRCCS Ca’ Granda - Ospedale Maggiore Policlinico; Milan Italy
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Guo K, Yao J, Yu Q, Li Z, Huang H, Cheng J, Wang Z, Zhu Y. The expression pattern of long non-coding RNA PVT1 in tumor tissues and in extracellular vesicles of colorectal cancer correlates with cancer progression. Tumour Biol 2017; 39:1010428317699122. [PMID: 28381186 DOI: 10.1177/1010428317699122] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The plasmacytoma variant translocation 1 gene (PVT1) is a large non-coding locus at adjacent of c-Myc, and long non-coding RNA PVT1 is now recognized as a cancerous gene co-amplified with c-Myc in various cancers. But the expression and functional role of PVT1 in colorectal cancer are still unelucidated. In addition, all the reported long non-coding RNAs so far are discovered in either cells or tissues, but no research about long non-coding RNAs detection in extracellular vesicles has been reported yet. In the present study, we firstly investigated the expression of PVT1 in colorectal cancer specimens and its correlation with the expression of c-Myc and other related genes by real-time polymerase chain reaction. Then, we isolated the extracellular vesicles from colorectal cancer cells culturing medium by differential centrifugation and detected the PVT1 expression in extracellular vesicles by using real-time polymerase chain reaction. The PVT1 targeting siRNA was transfected into SW480 and SW620 cells, and 3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium assay and flow cytometry were used to evaluate the cell proliferation and apoptosis. The results showed that the PVT1 expression in tumor tissues was higher than that in normal tissues, which was significantly correlated with the expression of c-Myc and three c-Myc regulating genes FUBP1, EZH2, and NPM1 and also correlated with the expression of two other PVT1-associated transcript factors nuclear factor-κB and myocyte-specific enhancer factor 2A. Here, we reported for the first time that PVT1 as a long non-coding RNA was successfully detected in extracellular vesicles excluded from SW620 and SW480 cells, and the expression level of PVT1 was higher in extracellular vesicles from the more aggressive cell SW620 than from SW480. The results also showed that by down-regulating the PVT1 expression, the c-Myc expression was suppressed, the cell proliferation was inhibited, and cell apoptosis was increased. Taken together, these findings implicated that PVT1 may be a new oncogene co-amplified with c-Myc in colorectal cancer tissues and extracellular vesicles and functionally correlated with the proliferation and apoptosis of colorectal cancer cells.
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Affiliation(s)
- Kai Guo
- Department of Gastroenterology, The 161th Hospital of PLA, Wuhan, China
| | - Jie Yao
- Department of Oncology, The 161th Hospital of PLA, Wuhan, China
| | - Qiang Yu
- Department of Hepatobiliary Surgery, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing, China
| | - Zijian Li
- Department of Oncology, The 161th Hospital of PLA, Wuhan, China
| | - Hu Huang
- Department of Oncology, The 161th Hospital of PLA, Wuhan, China
| | - Jianguo Cheng
- Department of Gastroenterology, The 161th Hospital of PLA, Wuhan, China
| | - Zhigang Wang
- Department of Oncology, The 161th Hospital of PLA, Wuhan, China
| | - Yunfeng Zhu
- Department of Hepatobiliary Surgery, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing, China
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Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
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Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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Cui C, Shu W, Li P. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications. Front Cell Dev Biol 2016; 4:89. [PMID: 27656642 PMCID: PMC5011256 DOI: 10.3389/fcell.2016.00089] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/11/2016] [Indexed: 12/14/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.
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Affiliation(s)
- Chenghua Cui
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of MedicineNew Haven, CT, USA; Department of Pathology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical SciencesTianjin, China
| | - Wei Shu
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of MedicineNew Haven, CT, USA; Department of Cell Biology and Genetics, Guangxi Medical UniversityNanning, China
| | - Peining Li
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of Medicine New Haven, CT, USA
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Rao PH, Zhao S, Zhao YJ, Yu A, Rainusso N, Trucco M, Allen-Rhoades W, Satterfield L, Fuja D, Borra VJ, Man TK, Donehower LA, Yustein JT. Coamplification ofMyc/Pvt1and homozygous deletion ofNlrp1locus are frequent genetics changes in mouse osteosarcoma. Genes Chromosomes Cancer 2015; 54:796-808. [DOI: 10.1002/gcc.22291] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/19/2015] [Accepted: 07/29/2015] [Indexed: 01/10/2023] Open
Affiliation(s)
- Pulivarthi H. Rao
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Shuying Zhao
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Yi-Jue Zhao
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Alexander Yu
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Nino Rainusso
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Matteo Trucco
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Wendy Allen-Rhoades
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Laura Satterfield
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
| | - Daniel Fuja
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
| | - Vishnupriya J. Borra
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Tsz-Kwong Man
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
| | - Lawrence A. Donehower
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
- Department of Molecular & Cellular Biology; Baylor College of Medicine; Houston TX 77030
- Department of Molecular Virology & Microbiology; Baylor College of Medicine; Houston TX 77030
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
| | - Jason T. Yustein
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics; Baylor College of Medicine; Houston TX 77030
- Department of Molecular & Cellular Biology; Baylor College of Medicine; Houston TX 77030
- Integrative Molecular and Biological Sciences Program; Baylor College of Medicine; Houston TX 77030
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10
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Xiang JF, Yang L, Chen LL. The long noncoding RNA regulation at the MYC locus. Curr Opin Genet Dev 2015; 33:41-8. [PMID: 26254776 DOI: 10.1016/j.gde.2015.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 07/15/2015] [Accepted: 07/20/2015] [Indexed: 01/17/2023]
Abstract
Aberrant expression of long noncoding RNAs (lncRNAs) has been linked to cancers. The MYC oncoprotein is a key contributor to the development of many human tumors. Recent studies have revealed that a number of lncRNAs originating from the human 8q24 locus previously known to corresponding to a 'gene desert' are transcribed and play important roles in MYC regulation. In this review, we highlight recent progress in how these lncRNAs participate in control of MYC levels in normal and tumor cells.
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Affiliation(s)
- Jian-Feng Xiang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China.
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11
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Matullo G, Guarrera S, Betti M, Fiorito G, Ferrante D, Voglino F, Cadby G, Di Gaetano C, Rosa F, Russo A, Hirvonen A, Casalone E, Tunesi S, Padoan M, Giordano M, Aspesi A, Casadio C, Ardissone F, Ruffini E, Betta PG, Libener R, Guaschino R, Piccolini E, Neri M, Musk AWB, de Klerk NH, Hui J, Beilby J, James AL, Creaney J, Robinson BW, Mukherjee S, Palmer LJ, Mirabelli D, Ugolini D, Bonassi S, Magnani C, Dianzani I. Genetic variants associated with increased risk of malignant pleural mesothelioma: a genome-wide association study. PLoS One 2013; 8:e61253. [PMID: 23626673 PMCID: PMC3634031 DOI: 10.1371/journal.pone.0061253] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/06/2013] [Indexed: 12/19/2022] Open
Abstract
Asbestos exposure is the main risk factor for malignant pleural mesothelioma (MPM), a rare aggressive tumor. Nevertheless, only 5-17% of those exposed to asbestos develop MPM, suggesting the involvement of other environmental and genetic risk factors. To identify the genetic risk factors that may contribute to the development of MPM, we conducted a genome-wide association study (GWAS; 370,000 genotyped SNPs, 5 million imputed SNPs) in Italy, among 407 MPM cases and 389 controls with a complete history of asbestos exposure. A replication study was also undertaken and included 428 MPM cases and 1269 controls from Australia. Although no single marker reached the genome-wide significance threshold, several associations were supported by haplotype-, chromosomal region-, gene- and gene-ontology process-based analyses. Most of these SNPs were located in regions reported to harbor aberrant alterations in mesothelioma (SLC7A14, THRB, CEBP350, ADAMTS2, ETV1, PVT1 and MMP14 genes), causing at most a 2-3-fold increase in MPM risk. The Australian replication study showed significant associations in five of these chromosomal regions (3q26.2, 4q32.1, 7p22.2, 14q11.2, 15q14). Multivariate analysis suggested an independent contribution of 10 genetic variants, with an Area Under the ROC Curve (AUC) of 0.76 when only exposure and covariates were included in the model, and of 0.86 when the genetic component was also included, with a substantial increase of asbestos exposure risk estimation (odds ratio, OR: 45.28, 95% confidence interval, CI: 21.52-95.28). These results showed that genetic risk factors may play an additional role in the development of MPM, and that these should be taken into account to better estimate individual MPM risk in individuals who have been exposed to asbestos.
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Affiliation(s)
- Giuseppe Matullo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Marta Betti
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | | | - Daniela Ferrante
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | | | - Gemma Cadby
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Nedlands, Western Australia, Australia
| | - Cornelia Di Gaetano
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Fabio Rosa
- Human Genetics Foundation, HuGeF, Turin, Italy
| | - Alessia Russo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Ari Hirvonen
- Centre of Expertise for Health and Work Ability, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Elisabetta Casalone
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Sara Tunesi
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marina Padoan
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Mara Giordano
- Laboratory of Genetics, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Anna Aspesi
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Caterina Casadio
- Thoracic Surgery Unit, University of Piemonte Orientale, Novara, Italy
| | - Francesco Ardissone
- Chest Surgery, Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Enrico Ruffini
- Thoracic Surgery Unit, University of Turin, Turin, Italy
| | - Pier Giacomo Betta
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberta Libener
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberto Guaschino
- Transfusion Centre, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Ezio Piccolini
- Pneumology Unit, Santo Spirito Hospital, Casale Monferrato, Italy
| | - Monica Neri
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Arthur W. B. Musk
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Nicholas H. de Klerk
- Centre for Child Health Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Jennie Hui
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - John Beilby
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Alan L. James
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Jenette Creaney
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Bruce W. Robinson
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sutapa Mukherjee
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Women's College Research Institute and Women's College Hospital, Toronto, Ontario, Canada
| | - Lyle J. Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - Dario Mirabelli
- Unit of Cancer Epidemiology, CPO-Piemonte and University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Donatella Ugolini
- Department of Internal Medicine, University of Genoa and IRCSS AOU San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Irma Dianzani
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
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Acute myeloid leukemia with promyelocytic morphology lacking RARA rearrangement and with double minutes, MYC deletion and 2 cell lines with amplification of MYC region: case report and literature review. J Hematop 2012. [DOI: 10.1007/s12308-012-0155-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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13
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Cavuoto P, Fenech MF. A review of methionine dependency and the role of methionine restriction in cancer growth control and life-span extension. Cancer Treat Rev 2012; 38:726-36. [PMID: 22342103 DOI: 10.1016/j.ctrv.2012.01.004] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 12/22/2011] [Accepted: 01/15/2012] [Indexed: 01/11/2023]
Abstract
Methionine is an essential amino acid with many key roles in mammalian metabolism such as protein synthesis, methylation of DNA and polyamine synthesis. Restriction of methionine may be an important strategy in cancer growth control particularly in cancers that exhibit dependence on methionine for survival and proliferation. Methionine dependence in cancer may be due to one or a combination of deletions, polymorphisms or alterations in expression of genes in the methionine de novo and salvage pathways. Cancer cells with these defects are unable to regenerate methionine via these pathways. Defects in the metabolism of folate may also contribute to the methionine dependence phenotype in cancer. Selective killing of methionine dependent cancer cells in co-culture with normal cells has been demonstrated using culture media deficient in methionine. Several animal studies utilizing a methionine restricted diet have reported inhibition of cancer growth and extension of a healthy life-span. In humans, vegan diets, which can be low in methionine, may prove to be a useful nutritional strategy in cancer growth control. The development of methioninase which depletes circulating levels of methionine may be another useful strategy in limiting cancer growth. The application of nutritional methionine restriction and methioninase in combination with chemotherapeutic regimens is the current focus of clinical studies.
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Affiliation(s)
- Paul Cavuoto
- CSIRO Food and Nutritional Sciences, P.O. Box 10041, Adelaide BC, SA 5000, Australia.
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14
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Barsotti AM, Beckerman R, Laptenko O, Huppi K, Caplen NJ, Prives C. p53-Dependent induction of PVT1 and miR-1204. J Biol Chem 2011; 287:2509-19. [PMID: 22110125 DOI: 10.1074/jbc.m111.322875] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
p53 is a tumor suppressor protein that acts as a transcription factor to regulate (either positively or negatively) a plethora of downstream target genes. Although its ability to induce protein coding genes is well documented, recent studies have implicated p53 in the regulation of non-coding RNAs, including both microRNAs (e.g. miR-34a) and long non-coding RNAs (e.g. lincRNA-p21). We have identified the non-protein coding locus PVT1 as a p53-inducible target gene. PVT1, a very large (>300 kb) locus located downstream of c-myc on chromosome 8q24, produces a wide variety of spliced non-coding RNAs as well as a cluster of six annotated microRNAs: miR-1204, miR-1205, miR-1206, miR-1207-5p, miR-1207-3p, and miR-1208. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assay (EMSA), and luciferase assays reveal that p53 binds and activates a canonical response element within the vicinity of miR-1204. Consistently, we demonstrate the p53-dependent induction of endogenous PVT1 transcripts and consequent up-regulation of mature miR-1204. Finally, we have shown that ectopic expression of miR-1204 leads to increased p53 levels and causes cell death in a partially p53-dependent manner.
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Affiliation(s)
- Anthony M Barsotti
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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15
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Forghieri F, Morselli M, Potenza L, Maccaferri M, Pedrazzi L, Coluccio V, Barozzi P, Vallerini D, Riva G, Zanetti E, Quarelli C, Bonacorsi G, Artusi T, Zaldini P, Zucchini P, Marasca R, Narni F, Falini B, Torelli G, Luppi M. A case of JAK2 V617F-positive myelodysplastic/myeloproliferative neoplasm with unusual morphology, resembling acute promyelocytic leukemia-like disorder with a chronic course. Leuk Lymphoma 2011; 52:2012-9. [PMID: 21635206 DOI: 10.3109/10428194.2011.584990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Bajaj R, Xu F, Xiang B, Wilcox K, Diadamo AJ, Kumar R, Pietraszkiewicz A, Halene S, Li P. Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia. Mol Cytogenet 2011; 4:3. [PMID: 21251322 PMCID: PMC3031273 DOI: 10.1186/1755-8166-4-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 01/20/2011] [Indexed: 12/16/2022] Open
Abstract
Background To evaluate the clinical validity of genome-wide oligonucleotide array comparative genomic hybridization (aCGH) for detecting somatic abnormalities, we have applied this genomic analysis to 30 cases (13 MDS and 17 AML) with clonal chromosomal abnormalities detected in more than 50% of analyzed metaphase cells. Results The aCGH detected all numerical chromosomal gains and losses from the mainline clones and 113 copy number alterations (CNAs) ranging from 0.257 to 102.519 megabases (Mb). Clinically significant recurrent deletions of 5q (involving the RPS14 gene), 12p12.3 (ETV6 gene), 17p13 (TP53 gene), 17q11.2 (NF1 gene) and 20q, double minutes containing the MYC gene and segmental amplification involving the MLL gene were further characterized with defined breakpoints and gene contents. Genomic features of microdeletions at 17q11.2 were confirmed by FISH using targeted BAC clones. The aCGH also defined break points in a derivative chromosome 6, der(6)t(3;6)(q21.3;p22.2), and an isodicentric X chromosome. However, chromosomally observed sideline clonal abnormalities in five cases were not detected by aCGH. Conclusions Our data indicated that an integrated cytogenomic analysis will be a better diagnostic scheme to delineate genomic contents of chromosomal and cryptic abnormalities in patients with MDS and AML. An evidence-based approach to interpret somatic genomic findings was proposed.
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Affiliation(s)
- Renu Bajaj
- Molecular Cytogenetics Laboratory, Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA.
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17
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Bruyère H, Sutherland H, Chipperfield K, Hudoba M. Concomitant and successive amplifications of MYC in APL-like leukemia. ACTA ACUST UNITED AC 2010; 197:75-80. [PMID: 20113841 DOI: 10.1016/j.cancergencyto.2009.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 10/26/2009] [Accepted: 11/02/2009] [Indexed: 11/15/2022]
Abstract
A 61-year-old male patient presented with very high blood white cell count, left shift of granulocytes to blasts, as well as low hemoglobin and platelets. The bone marrow aspirate and biopsy were consistent with an acute myeloid leukemia (AML). Blasts presented with large azurophilic inclusions and prominent Auer rods resembling acute promyelocytic leukemia (APL). Cytogenetic analysis revealed a deletion 9p and double-minute chromosomes. Fluorescence in situ hybridization showed amplification of the MYC probe and the absence of a RARA rearrangement. The patient achieved complete morphologic and cytogenetic remission 1 month after allogenic transplant, but relapsed 1 month later. Cytogenetics showed MYC amplification as a homogeneously staining region inserted into the long arm of one chromosome 9 and as a ring structure. At least five other acute promyelocytic leukemia-like cases without translocation 15;17, but with double minutes, have been reported in the literature. Only one of these had no RARA rearrangement. This report presents a second patient with APL-like bone marrow morphology, absence of RARA rearrangement, and MYC amplification. In this case, the amplification happened in various concomitant or successive forms.
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Affiliation(s)
- Hélène Bruyère
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada.
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