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Nabil R, Abdellateif MS, Gamal H, Hassan NM, Badawy RH, Ghareeb M, El Ashry MS. Clinical significance of EVI-1 gene expression and aberrations in patient with de-novo acute myeloid and acute lymphoid leukemia. Leuk Res 2023; 126:107019. [PMID: 36657369 DOI: 10.1016/j.leukres.2023.107019] [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: 11/17/2022] [Revised: 12/28/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
BACKGROUND Acute leukemia is a common health problem in adults and children, however its exact molecular etiology is still unclear. METHODS The expression of EVI-1 was assessed in the bone marrow of 178 de-novo acute leukemia patients (101 AML, 71 ALL and 6 MPAL), compared to 40 control subjects. EVI-1 gene aberrations were also assessed in 69 AML patients using Fluorescence in situ hybridization (FISH) technique. RESULTS The expression of EVI-1 was significantly lower in ALL patients compared to control [0.177 (0.002-15.189) vs 0.953 (0.179-1.68); respectively, P = 0.009]. There was no significant difference between AML patients and control group [0.150 (0.0-641) vs 0.953 (0.179-1.68); respectively, P = 0.082]. The sensitivity, specificity, AUC of EVI-1 in ALL were (80.3 %, 60 % and 0.778; respectively, P = 0.009), and (67.3 %, 60 %, 0.667; respectively P = 0.082) in AML patients. One patient showed EVI-1 gene rearrangement in a complex karyotype and four patients showed EVI-1 amplification in hyperdiploid karyotypes. All patients with BCR-ABL fusion were EVI-1 over-expressers (P = 0.010). AML patients with EVI-1 low expression were positively associated with t(8;21)(q22;q22)RUNX1:RUNX1T1 fusion, favorable recurrent translocation, and low genetic risk (P = 0.037, P = 0.023, and P = 0.013; respectively). There was a significant association between low EVI-1 expression and prolonged overall survival (OS) in AML patients, while there was no significant association with the disease-free survival (DFS) (P = 0.048 and P = 0.419). There was no significant impact of EVI-1 expression on OS and DFS rates in ALL patients. CONCLUSION EVI-1 expression could be a helpful diagnostic, prognostic, and predictive biomarker for acute leukemia especially in AML.
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Affiliation(s)
- Reem Nabil
- Clinical Pathology Department, National Cancer Institute, Cairo University, Egypt
| | - Mona S Abdellateif
- Medical Biochemistry and Molecular Biology, Cancer Biology Department, National Cancer Institute, Cairo University, Egypt.
| | - Hend Gamal
- Clinical Pathology Department, National Cancer Institute, Cairo University, Egypt
| | - Naglaa M Hassan
- Clinical Pathology Department, National Cancer Institute, Cairo University, Egypt
| | - Ragia H Badawy
- Clinical Pathology Department, National Cancer Institute, Cairo University, Egypt
| | - Mohamed Ghareeb
- Medical Oncology Department, National Cancer Institute, Cairo University, Egypt
| | - Mona S El Ashry
- Clinical Pathology Department, National Cancer Institute, Cairo University, Egypt
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An B, Xia J, Chang T, Wang X, Miao J, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle. Physiol Genomics 2018; 50:523-531. [DOI: 10.1152/physiolgenomics.00022.2018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.
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Affiliation(s)
- Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jiangwei Xia
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xiaoqiao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jian Miao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
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Wang B, Ye N, Cao SJ, Wen XT, Huang Y, Yan QG. Identification of novel and differentially expressed MicroRNAs in goat enzootic nasal adenocarcinoma. BMC Genomics 2016; 17:896. [PMID: 27825300 PMCID: PMC5101819 DOI: 10.1186/s12864-016-3238-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
Background MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in goats and sheep by enzootic nasal tumor virus (ENTV), is a chronic, progressive, contact transmitted disease. Methods In this work, small RNA Illumina high-throughput sequencing was used to construct a goat nasal miRNA library. This study aimed to identify novel and differentially expressed miRNAs in the tumor and para-carcinoma nasal tissues of Nanjiang yellow goats with ENA. Results Four hundred six known miRNAs and 29 novel miRNAs were identified. A total of 116 miRNAs were significantly differentially expressed in para-carcinoma nasal tissues and ENA (54 downregulated; 60 upregulated; two only expressed in control group); Target gene prediction and functional analysis revealed that 6176 non-redundancy target genes, 1792 significant GO and 97 significant KEGG pathway for 121 miRNAs (116 significant expression miRNAs and five star sequence) were predicted. GO and KEGG pathway analysis revealed the majority of target genes in ENA are involved in cell proliferation, signal transduction and other processes associated with cancer. Conclusions This is the first large-scale identification of miRNAs in Capra hircus ENA and provides a theoretical basis for investigating the complicated miRNA-mediated regulatory networks involved in the pathogenesis and progression of ENA. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3238-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bin Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Hui Min Road 211, Chengdu, Sichuan, 611130, People's Republic of China
| | - Ni Ye
- College of Veterinary Medicine, Sichuan Agricultural University, Hui Min Road 211, Chengdu, Sichuan, 611130, People's Republic of China
| | - San-Jie Cao
- College of Veterinary Medicine, Sichuan Agricultural University, Hui Min Road 211, Chengdu, Sichuan, 611130, People's Republic of China
| | - Xin-Tian Wen
- College of Veterinary Medicine, Sichuan Agricultural University, Hui Min Road 211, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yong Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Hui Min Road 211, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qi-Gui Yan
- College of Veterinary Medicine, Sichuan Agricultural University, Hui Min Road 211, Chengdu, Sichuan, 611130, People's Republic of China.
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Shen W, Clemente MJ, Hosono N, Yoshida K, Przychodzen B, Yoshizato T, Shiraishi Y, Miyano S, Ogawa S, Maciejewski JP, Makishima H. Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest 2014; 124:4529-38. [PMID: 25244093 DOI: 10.1172/jci74747] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/10/2014] [Indexed: 12/13/2022] Open
Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is a nonmalignant clonal disease of hematopoietic stem cells that is associated with hemolysis, marrow failure, and thrombophilia. PNH has been considered a monogenic disease that results from somatic mutations in the gene encoding PIGA, which is required for biosynthesis of glycosylphosphatidylinisotol-anchored (GPI-anchored) proteins. The loss of certain GPI-anchored proteins is hypothesized to provide the mutant clone with an extrinsic growth advantage, but some features of PNH argue that there are intrinsic drivers of clonal expansion. Here, we performed whole-exome sequencing of paired PNH+ and PNH- fractions on samples taken from 12 patients as well as targeted deep sequencing of an additional 36 PNH patients. We identified additional somatic mutations that resulted in a complex hierarchical clonal architecture, similar to that observed in myeloid neoplasms. In addition to mutations in PIGA, mutations were found in genes known to be involved in myeloid neoplasm pathogenesis, including TET2, SUZ12, U2AF1, and JAK2. Clonal analysis indicated that these additional mutations arose either as a subclone within the PIGA-mutant population, or prior to PIGA mutation. Together, our data indicate that in addition to PIGA mutations, accessory genetic events are frequent in PNH, suggesting a stepwise clonal evolution derived from a singular stem cell clone.
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Evi1 defines leukemia-initiating capacity and tyrosine kinase inhibitor resistance in chronic myeloid leukemia. Oncogene 2014; 33:5028-38. [PMID: 24747972 PMCID: PMC4217142 DOI: 10.1038/onc.2014.108] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 02/17/2014] [Accepted: 03/12/2014] [Indexed: 12/28/2022]
Abstract
Relapse of chronic myeloid leukemia (CML) is triggered by stem cells with a reconstituting capacity similar to that of hematopoietic stem cells (HSCs) and CML stem cells are a source of resistance in drug therapy with tyrosine kinase inhibitors (TKIs). Ecotropic viral integration site 1 (EVI1), a key transcription factor in HSC regulation, is known to predict poor outcomes in myeloid malignancies, however, incapability of prospective isolation of EVI1-high leukemic cells precludes the functional evaluation of intraindividual EVI1-high cells. Introduction of CML into Evi1-internal ribosomal entry site (IRES)-green fluorescent protein (GFP) knock-in mice, a versatile HSC-reporter strain, enables us to separate Evi1-high CML cells from the individual. Evi1-IRES-GFP allele models of CML in chronic phase (CML-CP), by retroviral overexpression of BCR-ABL and by crossing BCR-ABL transgenic mice, revealed that Evi1 is predominantly enriched in the stem cell fraction and associated with an enhanced proliferative as well as a leukemia-initiating capacity and that Evi1-high CML-CP cells exhibit resistance to TKIs. Overexpressing BCR-ABL and NUP98-HOXA9 in Evi1-IRES-GFP knock-in mice to model CML in blast crisis (CML-BC), in which Evi1-high cells turned to be a major population as opposed to a minor population in CML-CP models, showed that Evi1-high CML-BC cells have a greater potential to recapitulate the disease and appear resistant to TKIs. Furthermore, given that Evi1 heterozygosity ameliorates CML-CP and CML-BC development and that the combination of Evi1 and BCR-ABL causes acute myeloid leukemia resembling CML-BC, Evi1 could regulate CML development as a potent driver. In addition, in human CML-CP cases, we show that EVI1 is highly expressed in stem cell-enriched CD34+CD38-CD90+ fraction at single-cell level. This is the first report to clarify directly that Evi1-high leukemic cells themselves possess the superior potential to Evi1-low cells in oncogenic self-renewal, which highlights the role of Evi1 as a valuable and a functional marker of CML stem cells.
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EVI1 expression in childhood acute lymphoblastic leukaemia is not restricted to MLL and BCR/ABL rearrangements and is influenced by age. Blood Cancer J 2014; 4:e179. [PMID: 24464103 PMCID: PMC3913945 DOI: 10.1038/bcj.2013.76] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Manczinger M, Kemény L. Novel factors in the pathogenesis of psoriasis and potential drug candidates are found with systems biology approach. PLoS One 2013; 8:e80751. [PMID: 24303025 PMCID: PMC3841158 DOI: 10.1371/journal.pone.0080751] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/15/2013] [Indexed: 01/12/2023] Open
Abstract
Psoriasis is a multifactorial inflammatory skin disease characterized by increased proliferation of keratinocytes, activation of immune cells and susceptibility to metabolic syndrome. Systems biology approach makes it possible to reveal novel important factors in the pathogenesis of the disease. Protein-protein, protein-DNA, merged (containing both protein-protein and protein-DNA interactions) and chemical-protein interaction networks were constructed consisting of differentially expressed genes (DEG) between lesional and non-lesional skin samples of psoriatic patients and/or the encoded proteins. DEGs were determined by microarray meta-analysis using MetaOMICS package. We used STRING for protein-protein, CisRED for protein-DNA and STITCH for chemical-protein interaction network construction. General network-, cluster- and motif-analysis were carried out in each network. Many DEG-coded proteins (CCNA2, FYN, PIK3R1, CTGF, F3) and transcription factors (AR, TFDP1, MEF2A, MECOM) were identified as central nodes, suggesting their potential role in psoriasis pathogenesis. CCNA2, TFDP1 and MECOM might play role in the hyperproliferation of keratinocytes, whereas FYN may be involved in the disturbed immunity in psoriasis. AR can be an important link between inflammation and insulin resistance, while MEF2A has role in insulin signaling. A controller sub-network was constructed from interlinked positive feedback loops that with the capability to maintain psoriatic lesional phenotype. Analysis of chemical-protein interaction networks detected 34 drugs with previously confirmed disease-modifying effects, 23 drugs with some experimental evidences, and 21 drugs with case reports suggesting their positive or negative effects. In addition, 99 unpublished drug candidates were also found, that might serve future treatments for psoriasis.
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Affiliation(s)
- Máté Manczinger
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
- * E-mail:
| | - Lajos Kemény
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
- Dermatological Research Group of the Hungarian Academy of Sciences, Szeged, Hungary
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