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Zhuang H, Chen Y, Sheng X, Hong L, Gao R, Zhuang X. Searching for a signature involving 10 genes to predict the survival of patients with acute myelocytic leukemia through a combined multi-omics analysis. PeerJ 2020; 8:e9437. [PMID: 32617195 PMCID: PMC7321666 DOI: 10.7717/peerj.9437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/08/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Currently, acute myelocytic leukemia (AML) still has a poor prognosis. As a result, gene markers for predicting AML prognosis must be identified through systemic analysis of multi-omics data. METHODS First of all, the copy number variation (CNV), mutation, RNA-Seq, and single nucleotide polymorphism (SNP) data, as well as those clinical follow-up data, were obtained based on The Cancer Genome Atlas (TCGA) database. Thereafter, all samples (n = 229) were randomized as test set and training set, respectively. Of them, the training set was used to screen for genes related to prognosis, and genes with mutation, SNP or CNV. Then, shrinkage estimate was used for feature selection of all the as-screened genes, to select those stable biomarkers. Eventually, a prognosis model related to those genes was established, and validated within the GEO verification (n = 124 and 72) and test set (n = 127). Moreover, it was compared with the AML prognosis prediction model reported in literature. RESULTS Altogether 832 genes related to prognosis, 23 related to copy amplification, 774 associated with copy deletion, and 189 with significant genomic variations were acquired in this study. Later, genes with genomic variations and those related to prognosis were integrated to obtain 38 candidate genes; eventually, a shrinkage estimate was adopted to obtain 10 feature genes (including FAT2, CAMK2A, TCERG1, GDF9, PTGIS, DOC2B, DNTTIP1, PREX1, CRISPLD1 and C22orf42). Further, a signature was established using these 10 genes based on Cox regression analysis, and it served as an independent factor to predict AML prognosis. More importantly, it was able to stratify those external verification, test and training set samples with regard to the risk (P < 0.01). Compared with the prognosis prediction model reported in literature, the model established in this study was advantageous in terms of the prediction performance. CONCLUSION The signature based on 10 genes had been established in this study, which is promising to be used to be a new marker for predicting AML prognosis.
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Affiliation(s)
- Haifeng Zhuang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hang Zhou, China
| | - Yu Chen
- Hangzhou Medical College, Hang Zhou, China
| | - Xianfu Sheng
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hang Zhou, China
| | - Lili Hong
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hang Zhou, China
| | - Ruilan Gao
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hang Zhou, China
| | - Xiaofen Zhuang
- Hangzhou Fuyang Hospital of Traditional Chinese Medicine, Hang Zhou, China
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Sapienza MR, Fuligni F, Agostinelli C, Tripodo C, Righi S, Laginestra MA, Pileri A, Mancini M, Rossi M, Ricci F, Gazzola A, Melle F, Mannu C, Ulbar F, Arpinati M, Paulli M, Maeda T, Gibellini D, Pagano L, Pimpinelli N, Santucci M, Cerroni L, Croce CM, Facchetti F, Piccaluga PP, Pileri SA. Molecular profiling of blastic plasmacytoid dendritic cell neoplasm reveals a unique pattern and suggests selective sensitivity to NF-kB pathway inhibition. Leukemia 2014; 28:1606-16. [PMID: 24504027 PMCID: PMC4294271 DOI: 10.1038/leu.2014.64] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 01/07/2014] [Accepted: 01/28/2014] [Indexed: 12/12/2022]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare disease of controversial origin recently recognized as a neoplasm deriving from plasmacytoid dendritic cells (pDCs). Nevertheless, it remains an orphan tumor with obscure biology and dismal prognosis. To better understand the pathobiology of BPDCN and discover new targets for effective therapies, the gene expression profile (GEP) of 25 BPDCN samples was analyzed and compared with that of pDCs, their postulated normal counterpart. Validation was performed by immunohistochemistry (IHC), whereas functional experiments were carried out ex vivo. For the first time at the molecular level, we definitely recognized the cellular derivation of BPDCN that proved to originate from the myeloid lineage and in particular, from resting pDCs. Furthermore, thanks to an integrated bioinformatic approach we discovered aberrant activation of the NF-kB pathway and suggested it as a novel therapeutic target. We tested the efficacy of anti-NF-kB-treatment on the BPDCN cell line CAL-1, and successfully demonstrated by GEP and IHC the molecular shutoff of the NF-kB pathway. In conclusion, we identified a molecular signature representative of the transcriptional abnormalities of BPDCN and developed a cellular model proposing a novel therapeutic approach in the setting of this otherwise incurable disease.
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Affiliation(s)
- M R Sapienza
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - F Fuligni
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - C Agostinelli
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - C Tripodo
- Department of Health Science, Tumour Immunology Unit, Human Pathology Section University of Palermo School of Medicine, Palermo, Italy
| | - S Righi
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - M A Laginestra
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - A Pileri
- Department of Surgery and Translational Medicine - Division Dermatology, University of Florence, Florence, Italy
| | - M Mancini
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - M Rossi
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - F Ricci
- Department of Hematology, Oncology and Laboratory Medicine, Transfusion Medicine Service, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - A Gazzola
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - F Melle
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - C Mannu
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - F Ulbar
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - M Arpinati
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - M Paulli
- Anatomic Pathology Section, University of Pavia Medical School, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione Policlinico, San Matteo, Pavia, Italy
| | - T Maeda
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - D Gibellini
- Department of Experimental, Diagnostic, and Specialty Medicine, Microbiology Section, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - L Pagano
- Institute of Hematology, Catholic University, Rome, Italy
| | - N Pimpinelli
- Department of Surgery and Translational Medicine - Division Dermatology, University of Florence, Florence, Italy
| | - M Santucci
- Department of Surgery and Translational Medicine, Pathologic Anatomy Division, University of Florence, Florence, Italy
| | - L Cerroni
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - C M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - F Facchetti
- Department of Molecular and Translational Medicine, Pathology Section, University of Brescia, Brescia, Italy
| | - P P Piccaluga
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - S A Pileri
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
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