|
1
|
Padella A, Simonetti G, Paciello G, Giotopoulos G, Baldazzi C, Righi S, Ghetti M, Stengel A, Guadagnuolo V, De Tommaso R, Papayannidis C, Robustelli V, Franchini E, Ghelli Luserna di Rorà A, Ferrari A, Fontana MC, Bruno S, Ottaviani E, Soverini S, Storlazzi CT, Haferlach C, Sabattini E, Testoni N, Iacobucci I, Huntly BJP, Ficarra E, Martinelli G. Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia. Cancers (Basel) 2019; 11:E1951. [PMID: 31817495 PMCID: PMC6966504 DOI: 10.3390/cancers11121951] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately 18% of acute myeloid leukemia (AML) cases express a fusion transcript. However, few fusions are recurrent across AML and the identification of these rare chimeras is of interest to characterize AML patients. Here, we studied the transcriptome of 8 adult AML patients with poorly described chromosomal translocation(s), with the aim of identifying novel and rare fusion transcripts. We integrated RNA-sequencing data with multiple approaches including computational analysis, Sanger sequencing, fluorescence in situ hybridization and in vitro studies to assess the oncogenic potential of the ZEB2-BCL11B chimera. We detected 7 different fusions with partner genes involving transcription factors (OAZ-MAFK, ZEB2-BCL11B), tumor suppressors (SAV1-GYPB, PUF60-TYW1, CNOT2-WT1) and rearrangements associated with the loss of NF1 (CPD-PXT1, UTP6-CRLF3). Notably, ZEB2-BCL11B rearrangements co-occurred with FLT3 mutations and were associated with a poorly differentiated or mixed phenotype leukemia. Although the fusion alone did not transform murine c-Kit+ bone marrow cells, 45.4% of 14q32 non-rearranged AML cases were also BCL11B-positive, suggesting a more general and complex mechanism of leukemogenesis associated with BCL11B expression. Overall, by combining different approaches, we described rare fusion events contributing to the complexity of AML and we linked the expression of some chimeras to genomic alterations hitting known genes in AML.
Collapse
Affiliation(s)
- Antonella Padella
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Giorgia Simonetti
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Giulia Paciello
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino, 10129 Turin, Italy; (G.P.); (E.F.)
| | - George Giotopoulos
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, UK; (G.G.); (B.J.P.H.)
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke’s Hospital, University of Cambridge, Cambridge CB2 0XY, UK
| | - Carmen Baldazzi
- Institute of Hematology “L. and A. Seràgnoli”, Sant’Orsola-Malpighi University Hospital, 40138 Bologna, Italy;
| | - Simona Righi
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Martina Ghetti
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Anna Stengel
- MLL-Munich Leukemia Laboratory, 81377 Munich, Germany; (A.S.); (C.H.)
| | - Viviana Guadagnuolo
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Rossella De Tommaso
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Valentina Robustelli
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Eugenia Franchini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Andrea Ghelli Luserna di Rorà
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Anna Ferrari
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| | - Maria Chiara Fontana
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Samantha Bruno
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Emanuela Ottaviani
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Simona Soverini
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | | | - Claudia Haferlach
- MLL-Munich Leukemia Laboratory, 81377 Munich, Germany; (A.S.); (C.H.)
| | - Elena Sabattini
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Nicoletta Testoni
- Department of Experimental, Diagnostic and Speciality Medicine, University of Bologna, 40138 Bologna, Italy; (A.P.); (S.R.); (V.G.); (R.D.T.); (C.P.); (V.R.); (M.C.F.); (S.B.); (E.O.); (S.S.); (E.S.); (N.T.)
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Brian J. P. Huntly
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1TN, UK; (G.G.); (B.J.P.H.)
- Department of Haematology, Cambridge Institute for Medical Research and Addenbrooke’s Hospital, University of Cambridge, Cambridge CB2 0XY, UK
| | - Elisa Ficarra
- Department of Control and Computer Engineering DAUIN, Politecnico di Torino, 10129 Turin, Italy; (G.P.); (E.F.)
| | - Giovanni Martinelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy; (G.S.); (M.G.); (E.F.); (A.G.L.d.R.); (A.F.)
| |
Collapse
|
|
2
|
Hoff NP, Degrandi D, Hengge U, Pfeffer K, Wurthner JU. Carboxypeptidase D: A Novel TGF-β Target Gene Dysregulated in Patients with Lupus Erythematosus. J Clin Immunol 2007; 27:568-79. [PMID: 17641957 DOI: 10.1007/s10875-007-9118-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2007] [Accepted: 06/25/2007] [Indexed: 10/23/2022]
Abstract
Transforming growth factor-beta (TGF-beta) is a multifunctional cytokine that mainly acts as an inhibitor of immune functions. A lack of functional TGF-beta leads to autoimmune disease in animal models and dysregulated TGF-beta signaling is implicated in human autoimmune diseases. To define target genes that play a part in the inhibitory role of TGF-beta in the immune system, we have identified genes stimulated by TGF-beta in macrophages by gene-chip analysis. One of the TGF-beta regulated genes is carboxypeptidase D (CpD), a 180-kDa type I membrane protein. We have demonstrated that CpD is regulated by TGF-beta in various cell types of both, murine and human origin and, interestingly, is significantly downregulated in CD14 positive cells isolated from patients with lupus erythematosus (LE). Moreover, we show that downregulation of CpD leads to downmodulation of TGF-beta itself, suggesting a role for CpD in a positive feedback loop, providing further evidence for a role of this enzyme in LE. To our knowledge, this is the first report that demonstrates carboxypeptidase D as a TGF-beta target gene that is implicated in the pathogenesis of LE.
Collapse
Affiliation(s)
- Norman-Philipp Hoff
- Institute for Medical Microbiology, University of Duesseldorf, 40225, Duesseldorf, Germany.
| | | | | | | | | |
Collapse
|
|
3
|
Matthews KW, Mueller-Ortiz SL, Wetsel RA. Carboxypeptidase N: a pleiotropic regulator of inflammation. Mol Immunol 2004; 40:785-93. [PMID: 14687935 DOI: 10.1016/j.molimm.2003.10.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Carboxypeptidase N (CPN) is a plasma zinc metalloprotease, which consists of two enzymatically active small subunits (CPN1) and two large subunits (CPN2) that protect the protein from degradation. CPN cleaves carboxy-terminal arginines and lysines from peptides found in the bloodstream such as complement anaphylatoxins, kinins, and creatine kinase MM (CK-MM). By removing only one amino acid, CPN has the ability to change peptide activity and receptor binding. CPN is a member of a larger family of carboxypeptidases, many of which also cleave arginine and lysine. Because of the highly conserved active sites and the possible redundant functions of carboxypeptidases, it has been difficult to elucidate the role of CPN in disease processes. The future use of gene ablation technology may be the most appropriate way to understand the function of CPN in vivo.
Collapse
Affiliation(s)
- Kirstin W Matthews
- Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas-Houston, 2121 West Holcombe Blvd, Houston, TX 77030, USA
| | | | | |
Collapse
|
|
4
|
Timblin B, Rehli M, Skidgel RA. Structural characterization of the human carboxypeptidase D gene and its promoter. Int Immunopharmacol 2002; 2:1907-17. [PMID: 12489804 DOI: 10.1016/s1567-5769(02)00149-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Human carboxypeptidase D (CPD) is a 180-kDa type I membrane protein with three tandem active site domains. CPD is a B-type (or kininase I-type) carboxypeptidase that cleaves C-terminal basic residues from proteins and peptides, such as Arg9 from bradykinin. The human carboxypeptidase D (CPD) gene was found to encompass approximately 88.3 kb of genomic sequence, containing 21 exons ranging in size from 65 to 1813 bp, and 21 introns ranging in size from 112 bp to 35.6 kb. Although CPD and CPM belong to the same metallocarboxypeptidase subfamily, their intron/exon structures differ significantly. Multiple transcription start sites were found in the CPD gene within a GC-rich sequence lacking the typical TATA box, but containing three GC boxes. Luciferase reporter assays with various size constructs containing the promoter region upstream of the start sites showed that it was active in three different cell lines, especially in the human hepatoma cell line HepG2 and the human monocytic cell line THP-1, which have high constitutive expression of CPD.
Collapse
Affiliation(s)
- Barbara Timblin
- Department of Pharmacology, College of Medicine, University of Illinois, Chicago, IL 60612, USA
| | | | | |
Collapse
|
|
5
|
Matthews KW, Wetsel RA. Characterization of mouse carboxypeptidase N small active subunit gene structure. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 166:6196-202. [PMID: 11342641 DOI: 10.4049/jimmunol.166.10.6196] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Carboxypeptidase N (CPN) is a plasma zinc metalloprotease comprised of two small subunits that have enzymatic activity, and two large subunits, which protect the enzyme from degradation. CPN cleaves the carboxyl-terminal amino acids arginine and lysine from biologically active peptides such as complement anaphylatoxins, kinins, and fibrinopeptides. To delineate the murine CPN small subunit coding region, gene structure, and chromosome location, cDNA and genomic clones were isolated, characterized, and used in Northern and fluorescence in situ hybridization analyses. The results from this study demonstrate that the murine CPN small subunit gene is a single copy gene of approximately 29 kb that is transcribed in the liver into a 1793-bp mRNA with an open reading frame of 1371 nucleotides encoding 457 aa. The gene contains nine exons ranging in size from 455 bp (exon 1) to 100 bp (exon 7), and eight introns ranging in size from 6.2 kb (intron 2) to 1.4 kb (intron 4). All intron/exon junctions follow the normal consensus rule. The mouse CPN small subunit gene localized to chromosomal band 19D2, which is syntenic to human chromosome 10q23-25. Primer extension experiments using mouse liver mRNA indicate one major transcriptional initiation site and three minor sites. Sequence analysis of the 5'-flanking region indicated a TATA-less promoter and numerous transcription factor binding sites, which may confer liver-specific expression of the CPN small subunit gene.
Collapse
Affiliation(s)
- K W Matthews
- University of Texas-Houston Institute of Molecular Medicine for the Prevention of Human Diseases, and Department of Biochemistry and Molecular Biology, University of Texas-Houston Medical School, Houston, TX 77030, USA
| | | |
Collapse
|