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Kao TW, Chen HH, Lin J, Wang TL, Shen YA. PBX1 as a novel master regulator in cancer: Its regulation, molecular biology, and therapeutic applications. Biochim Biophys Acta Rev Cancer 2024; 1879:189085. [PMID: 38341110 DOI: 10.1016/j.bbcan.2024.189085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
PBX1 is a critical transcription factor at the top of various cell fate-determining pathways. In cancer, PBX1 stands at the crossroads of multiple oncogenic signaling pathways and mediates responses by recruiting a broad repertoire of downstream targets. Research thus far has corroborated the involvement of PBX1 in cancer proliferation, resisting apoptosis, tumor-associated neoangiogenesis, epithelial-mesenchymal transition (EMT) and metastasis, immune evasion, genome instability, and dysregulating cellular metabolism. Recently, our understanding of the functional regulation of the PBX1 protein has advanced, as increasing evidence has depicted a regulatory network consisting of transcriptional, post-transcriptional, and post-translational levels of control mechanisms. Furthermore, accumulating studies have supported the clinical utilization of PBX1 as a prognostic or therapeutic target in cancer. Preliminary results showed that PBX1 entails vast potential as a targetable master regulator in the treatment of cancer, particularly in those with high-risk features and resistance to other therapeutic strategies. In this review, we will explore the regulation, protein-protein interactions, molecular pathways, clinical application, and future challenges of PBX1.
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Affiliation(s)
- Ting-Wan Kao
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Hsiao-Han Chen
- Department of General Medicine, National Taiwan University Hospital, Taipei 100224, Taiwan
| | - James Lin
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Tian-Li Wang
- Departments of Pathology, Oncology and Gynecology and Obstetrics, Johns Hopkins Medical Institutions, 1550 Orleans Street, CRB2, Room 306, Baltimore, MD 21231, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yao-An Shen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan; International Master/Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan.
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2
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Meriç N, Albayrak E, Gülbaş Z, Kocabaş F. MEIS inhibitors reduce the viability of primary leukemia cells and Stem cells by inducing apoptosis. Leuk Lymphoma 2024; 65:187-198. [PMID: 37902585 DOI: 10.1080/10428194.2023.2275532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/22/2023] [Indexed: 10/31/2023]
Abstract
Leukemia stem cells (LSCs) exhibit self-renewal, resistance to standard treatments, and involvement in leukemia relapse. Higher Myeloid Ecotropic Integration Site-1 (MEIS1) expression in leukemic blast samples has been linked to resistance to conventional treatment. We studied the MEIS1 and associated factors in relapsed LSCs and assessed the effect of recently developed MEIS inhibitors (MEISi). Meis1 gene expression was found to be higher in patients with leukemia and relapsed samples. The majority of CD123+ and CD34+ LSCs demonstrated higher MEIS1/2/3 content. Depending on the patient chemotherapy regimen, Meis1 expression increased in relapsed samples. Although there are increased Meis2, Meis3, Hoxa9, Pbx1, or CD34 expressions in the relapsed patients, they are not correlated with Meis1 content in every patient or regimen. MEISi has reduced MEIS1 transcriptional activity and LSC cell survival by apoptosis. Pharmacological targeting with MEISi in LSCs could have a potential effect in limiting leukemia relapse and chemotherapeutic resistance.
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Affiliation(s)
- Neslihan Meriç
- Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, Kütahya Health Sciences, University, Kütahya, Türkiye
| | - Esra Albayrak
- Center of Stem Cell Research and Application, 19 Mayıs University, Samsun, Türkiye
| | - Zafer Gülbaş
- Anadolu Medical Center Hospital, Bone Marrow Transplantation Unit, Kocaeli, Türkiye
| | - Fatih Kocabaş
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Türkiye
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3
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Bastone AL, Dziadek V, John-Neek P, Mansel F, Fleischauer J, Agyeman-Duah E, Schaudien D, Dittrich-Breiholz O, Schwarzer A, Schambach A, Rothe M. Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants. Mol Ther Methods Clin Dev 2023; 30:515-533. [PMID: 37693949 PMCID: PMC10491817 DOI: 10.1016/j.omtm.2023.08.017] [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: 10/24/2022] [Accepted: 08/18/2023] [Indexed: 09/12/2023]
Abstract
Safety assessment in retroviral vector-mediated gene therapy remains challenging. In clinical trials for different blood and immune disorders, insertional mutagenesis led to myeloid and lymphoid leukemia. We previously developed the In Vitro Immortalization Assay (IVIM) and Surrogate Assay for Genotoxicity Assessment (SAGA) for pre-clinical genotoxicity prediction of integrating vectors. Murine hematopoietic stem and progenitor cells (mHSPCs) transduced with mutagenic vectors acquire a proliferation advantage under limiting dilution (IVIM) and activate stem cell- and cancer-related transcriptional programs (SAGA). However, both assays present an intrinsic myeloid bias due to culture conditions. To detect lymphoid mutants, we differentiated mHSPCs to mature T cells and analyzed their phenotype, insertion site pattern, and gene expression changes after transduction with retroviral vectors. Mutagenic vectors induced a block in differentiation at an early progenitor stage (double-negative 2) compared to fully differentiated untransduced mock cultures. Arrested samples harbored high-risk insertions close to Lmo2, frequently observed in clinical trials with severe adverse events. Lymphoid insertional mutants displayed a unique gene expression signature identified by SAGA. The gene expression-based highly sensitive molecular readout will broaden our understanding of vector-induced oncogenicity and help in pre-clinical prediction of retroviral genotoxicity.
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Affiliation(s)
- Antonella L. Bastone
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Violetta Dziadek
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Philipp John-Neek
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Friederike Mansel
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Jenni Fleischauer
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Eric Agyeman-Duah
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Dirk Schaudien
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Hannover, Germany
| | | | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Rothe
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH – Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
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Zhang G, Xu X, Zhu L, Li S, Chen R, Lv N, Li Z, Wang J, Li Q, Zhou W, Yang P, Liu J. A Novel Molecular Classification Method for Glioblastoma Based on Tumor Cell Differentiation Trajectories. Stem Cells Int 2023; 2023:2826815. [PMID: 37964983 PMCID: PMC10643041 DOI: 10.1155/2023/2826815] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2023] Open
Abstract
The latest 2021 WHO classification redefines glioblastoma (GBM) as the hierarchical reporting standard by eliminating glioblastoma, IDH-mutant and only retaining the tumor entity of "glioblastoma, IDH-wild type." Knowing that subclassification of tumors based on molecular features is supposed to facilitate the therapeutic choice and increase the response rate in cancer patients, it is necessary to carry out molecular classification of the newly defined GBM. Although differentiation trajectory inference based on single-cell sequencing (scRNA-seq) data holds great promise for identifying cell heterogeneity, it has not been used in the study of GBM molecular classification. Single-cell transcriptome sequencing data from 10 GBM samples were used to identify molecular classification based on differentiation trajectories. The expressions of identified features were validated by public bulk RNA-sequencing data. Clinical feasibility of the classification system was examined in tissue samples by immunohistochemical (IHC) staining and immunofluorescence, and their clinical significance was investigated in public cohorts and clinical samples with complete clinical follow-up information. By analyzing scRNA-seq data of 10 GBM samples, four differentiation trajectories from the glioblastoma stem cell-like (GSCL) cluster were identified, based on which malignant cells were classified into five characteristic subclusters. Each cluster exhibited different potential drug sensitivities, pathways, functions, and transcriptional modules. The classification model was further examined in TCGA and CGGA datasets. According to the different abundance of five characteristic cell clusters, the patients were classified into five groups which we named Ac-G, Class-G, Neo-G, Opc-G, and Undiff-G groups. It was found that the Undiff-G group exhibited the worst overall survival (OS) in both TCGA and CGGA cohorts. In addition, the classification model was verified by IHC staining in 137 GBM samples to further clarify the difference in OS between the five groups. Furthermore, the novel biomarkers of glioblastoma stem cells (GSCs) were also described. In summary, we identified five classifications of GBM and found that they exhibited distinct drug sensitivities and different prognoses, suggesting that the new grouping system may be able to provide important prognostic information and have certain guiding significance for the treatment of GBM, and identified the GSCL cluster in GBM tissues and described its characteristic program, which may help develop new potential therapeutic targets for GSCs in GBM.
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Affiliation(s)
- Guanghao Zhang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xiaolong Xu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Luojiang Zhu
- Neurosurgery Department, 922th Hospital of Joint Logistics Support Force, PLA, China
| | - Sisi Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Rundong Chen
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Nan Lv
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Zifu Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jing Wang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Qiang Li
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Wang Zhou
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Pengfei Yang
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jianmin Liu
- Neurovascular Center, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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5
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Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis. Biomolecules 2022; 12:biom12060822. [PMID: 35740947 PMCID: PMC9221482 DOI: 10.3390/biom12060822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 02/05/2023] Open
Abstract
PBX4 belongs to the pre-B-cell leukemia homeobox (PBX) transcription factors family and acts as a transcriptional cofactor of HOX proteins participating in several pathophysiological processes. Recent studies have revealed that the dysregulation of PBX4 is closely related to multiple diseases, especially cancers. However, the research on PBX4’s potential roles in 33 cancers from the Cancer Genome Atlas (TCGA) is still insufficient. Therefore, we performed a comprehensive pan-cancer analysis to explore the roles of PBX4with multiple public databases. Our results showed that PBX4 was differentially expressed in 17 types of human cancer and significantly correlated to the pathological stage, tumor grade, and immune and molecular subtypes. We used the Kaplan–Meier plotter and PrognoScan databases to find the significant associations between PBX4 expression and prognostic values of multiple cancers. It was also found that PBX4 expression was statistically related to mutation status, DNA methylation, immune infiltration, drug sensitivity, and immune checkpoint blockade (ICB) therapy. Additionally, we found that PBX4 was involved in different functional states of multiple cancers from the single-cell resolution perspective. Enrichment analysis results showed that PBX4-related genes were enriched in the cell cycle process, MAPK cascade, ncRNA metabolic process, positive regulation of GTPase activity, and regulation of lipase activity and mainly participated in the pathways of cholesterol metabolism, base excision repair, herpes simplex virus 1 infection, transcriptional misregulation in cancer, and Epstein–Barr virus infection. Altogether, our integrative analysis could help in better understanding the potential roles of PBX4 in different human cancers.
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6
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Meriç N, Kocabaş F. The Historical Relationship Between Meis1 and Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1387:127-144. [DOI: 10.1007/5584_2021_705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Yao M, Gu Y, Yang Z, Zhong K, Chen Z. MEIS1 and its potential as a cancer therapeutic target (Review). Int J Mol Med 2021; 48:181. [PMID: 34318904 PMCID: PMC8354308 DOI: 10.3892/ijmm.2021.5014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/08/2021] [Indexed: 01/26/2023] Open
Abstract
Meis homeobox 1 (Meis1) was initially discovered in 1995 as a factor involved in leukemia in an animal model. Subsequently, 2 years later, MEIS1, the human homolog, was cloned in the liver and cerebellum, and was found to be highly expressed in myeloid leukemia cells. The MEIS1 gene, located on chromosome 2p14, encodes a 390-amino acid protein with six domains. The expression of homeobox protein MEIS1 is affected by cell type, age and environmental conditions, as well as the pathological state. Certain types of modifications of MEIS1 and its protein interaction with homeobox or pre-B-cell leukemia homeobox proteins have been described. As a transcription factor, MEIS1 protein is involved in cell proliferation in leukemia and some solid tumors. The present review article discusses the molecular biology, modifications, protein-protein interactions, as well as the role of MEIS1 in cell proliferation of cancer cells and MEIS1 inhibitors. It is suggested by the available literature MEIS1 has potential to become a cancer therapeutic target.
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Affiliation(s)
- Maozhong Yao
- Clinical Research Center, Hainan Provincial Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Haikou, Hainan 570203, P.R. China
| | - Yong Gu
- Clinical Research Center, Hainan Provincial Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Haikou, Hainan 570203, P.R. China
| | - Zhaoxin Yang
- Teaching Experimental Animal Center, Research Center for Drug Safety Evaluation of Hainan Province, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Keyan Zhong
- Teaching Experimental Animal Center, Research Center for Drug Safety Evaluation of Hainan Province, Hainan Medical University, Haikou, Hainan 571199, P.R. China
| | - Zhanjuan Chen
- Chemical Experiment Teaching Center, College of Pharmacy, Hainan Medical University, Haikou, Hainan 571199, P.R. China
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8
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Lin J, Zhu H, Hong L, Tang W, Wang J, Hu H, Wu X, Chen Y, Liu G, Yang Q, Li J, Wang Y, Lin Z, Xiao Y, Dai W, Huang M, Li G, Li A, Wang J, Xiang L, Liu S. Coexpression of HOXA6 and PBX2 promotes metastasis in gastric cancer. Aging (Albany NY) 2021; 13:6606-6624. [PMID: 33535170 PMCID: PMC7993744 DOI: 10.18632/aging.202426] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 11/03/2020] [Indexed: 01/23/2023]
Abstract
HOXA6 gene plays a role of the oncogene in various cancers. Nonetheless, its effect on gastric cancer (GC) occurrence and development is still unclear. We analysed whether HOXA6 interacts with the PBX2 protein using the STRING database. The molecular mechanism by which HOXA6 synergizes with PBX2 in GC metastasis is not fully understood. Here, we found that the expression of HOXA6 was increased in GC tissues and cell lines. The upregulation of HOXA6 was closely associated with differentiation, lymph node metastasis, AJCC stage, TNM stage, and poor survival outcome in GC patients based on tissue microarray (TMA) data. Moreover, the overexpression of HOXA6 promoted, whereas siRNA-mediated repression of HOXA6 inhibited, the cell proliferation, migration, and invasion of GC cells. Furthermore, HOXA6 could physically interact with and stabilize PBX2. In addition, HOXA6 and PBX2 expression was positively correlated in GC cells and tissue. HOXA6 and PBX2 suppression in GC cells also led to decreased migration and invasion potential in vitro. In vivo, HOXA6 was shown to cooperate with PBX2 to enhance cell metastasis via orthotopic implantation. These data indicate that HOXA6 promotes cell proliferation, migration, and invasion and that the HOXA6-PBX2 axis may be a useful biomarker for disease progression in GC.
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Affiliation(s)
- Jianjiao Lin
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Gastroenterology, Longgang District People’s Hospital, Shenzhen 518172, China
| | - Huiqiong Zhu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Linjie Hong
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Weimei Tang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jing Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hongsong Hu
- Department of Gastroenterology, Longgang District People’s Hospital, Shenzhen 518172, China
| | - Xiaosheng Wu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yaying Chen
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Gastroenterology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510515, China
| | - Guangnan Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qiong Yang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- The Second Affiliated Hospital of University of South China, Hengyang 421001, China
| | - Jiaying Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yusi Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhizhao Lin
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yizhi Xiao
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Weiyu Dai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Miaojvan Huang
- Department of Gastroenterology, Longgang District People’s Hospital, Shenzhen 518172, China
| | - Guoxin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Aimin Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jide Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Gastroenterology, Longgang District People’s Hospital, Shenzhen 518172, China
| | - Li Xiang
- Department of Gastroenterology, Longgang District People’s Hospital, Shenzhen 518172, China
| | - Side Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Department of Gastroenterology, Longgang District People’s Hospital, Shenzhen 518172, China
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Bruckmann C, Tamburri S, De Lorenzi V, Doti N, Monti A, Mathiasen L, Cattaneo A, Ruvo M, Bachi A, Blasi F. Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis. Sci Rep 2020; 10:16809. [PMID: 33033354 PMCID: PMC7545097 DOI: 10.1038/s41598-020-74032-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/25/2020] [Indexed: 02/08/2023] Open
Abstract
Both onco-suppressor PREP1 and the oncogene MEIS1 bind to PBX1. This interaction stabilizes the two proteins and allows their translocation into the nucleus and thus their transcriptional activity. Here, we have combined cross-linking mass-spectrometry and systematic mutagenesis to detail the binding geometry of the PBX1-PREP1 (and PBX1-MEIS1) complexes, under native in vivo conditions. The data confirm the existence of two distinct interaction sites within the PBC domain of PBX1 and unravel differences among the highly similar binding sites of MEIS1 and PREP1. The HR2 domain has a fundamental role in binding the PBC-B domain of PBX1 in both PREP1 and MEIS1. The HR1 domain of MEIS1, however, seem to play a less stringent role in PBX1 interaction with respect to that of PREP1. This difference is also reflected by the different binding affinity of the two proteins to PBX1. Although partial, this analysis provides for the first time some ideas on the tertiary structure of the complexes not available before. Moreover, the extensive mutagenic analysis of PREP1 identifies the role of individual hydrophobic HR1 and HR2 residues, both in vitro and in vivo.
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Affiliation(s)
- Chiara Bruckmann
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
| | - Simone Tamburri
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Valentina De Lorenzi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56124, Pisa, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Lisa Mathiasen
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Angela Cattaneo
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
- Cogentech S.R.L. Benefit Corporation IT, Via Adamello 16, 20139, Milan, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Angela Bachi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy
| | - Francesco Blasi
- IFOM (Foundation FIRC Institute of Molecular Oncology), Via Adamello 16, 20139, Milan, Italy.
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10
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Ao X, Ding W, Ge H, Zhang Y, Ding D, Liu Y. PBX1 is a valuable prognostic biomarker for patients with breast cancer. Exp Ther Med 2020; 20:385-394. [PMID: 32565927 PMCID: PMC7286203 DOI: 10.3892/etm.2020.8705] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Pre-B-cell leukemia transcription factor (PBX) proteins have important roles in the development of numerous organs. To date, four members of the PBX family have been identified to be involved in human cancer but little is known about their expression patterns and precise functions in breast cancer (BC) progression. The aim of the present study was to determine whether they have the potential to be prognostic biomarkers in patients with BC. The expression patterns of PBXs were evaluated using Oncomine, Cancer Cell Line Encyclopedia and Gene expression-based Outcome for Breast cancer Online algorithm analyses. The prognostic value of PBX1 was determined by Kaplan-Meier plotter analysis. It was observed that, among all PBX family members, only PBX1 was significantly upregulated in BC vs. normal tissues. Meta-analysis in the Oncomine database revealed that PBX1 was significantly upregulated in invasive breast carcinoma stroma, ductal breast carcinoma, invasive lobular breast carcinoma, invasive mixed breast carcinoma and male breast carcinoma compared with normal tissues. In addition, PBX1 was significantly correlated with forkhead box protein A1. Subtype analysis indicated that PBX1 overexpression was associated with luminal-like and hormone receptor-sensitive subtypes. In the survival analysis, a high expression level of PBX1 was associated with poor prognosis of patients with estrogen receptor (ER)-positive, luminal A and luminal B subtypes of BC. The results of the present study indicate that PBX1 may serve as a specific biomarker and essential prognostic factor for ER-positive, luminal A and luminal B subtypes of BC.
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Affiliation(s)
- Xiang Ao
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Wei Ding
- Department of Comprehensive Internal Medicine, Affiliated Hospital, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Hu Ge
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China.,Department of Molecular Informatics, Hengrui Pharmaceutical Co., Ltd., Shanghai 200245, P.R. China
| | - Yuan Zhang
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Dan Ding
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Ying Liu
- Center for Precision Medicine, Institute for Translational Medicine, College of Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
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Expanding the Spectrum of Intraosseous Rhabdomyosarcoma: Correlation Between 2 Distinct Gene Fusions and Phenotype. Am J Surg Pathol 2020; 43:695-702. [PMID: 30720533 DOI: 10.1097/pas.0000000000001227] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Primary intraosseous rhabdomyosarcomas (RMSs) are extremely rare. Recently 2 studies reported 4 cases of primary intraosseous RMS with EWSR1/FUS-TFCP2 gene fusions, associated with somewhat conflicting histologic features, ranging from spindle to epithelioid. In this study we sought to further investigate the pathologic and molecular abnormalities of a larger group of intraosseous RMSs by a combined approach using targeted RNA sequencing analysis and fluorescence in situ hybridization (FISH). We identified 7 cases, 3 males and 4 females, all in young adults, age range 20 to 39 years (median, 27 y). Three cases involved the pelvis, 2 involved the femur and 1 each involved the maxilla and the skull. Molecular studies identified recurrent gene fusions in all 7 cases tested, including: a novel MEIS1-NCOA2 fusion in 2 cases, EWSR1-TFCP2 in 3 cases, and FUS-TFCP2 gene fusions in 1 case. One case showed a FUS gene rearrangement, without a TFCP2 gene abnormality by FISH. The MEIS1-NCOA2-positive cases were characterized by a more primitive and fascicular spindle cell appearance, while the EWSR1/FUS rearranged tumors had a hybrid spindle and epithelioid phenotype, with more abundant eosinophilic cytoplasm and mild nuclear pleomorphism. Immunohistochemically, all tumors were positive for desmin and myogenin (focal). In addition, 4 tumors with TFCP2-associated gene fusions also coexpressed ALK and cytokeratin. In conclusion, our results suggest a high incidence of gene fusions in primary RMSs of bone, with 2 molecular subsets emerging, defined by either MEIS1-NCOA2 or EWSR1/FUS-TFCP2 fusions, showing distinct morphology and immunophenotype. Additional studies with larger numbers of cases and longer follow-up data are required to definitively evaluate the biological behavior of these tumors and to establish their relationship to other spindle cell RMS genetic groups.
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12
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Kanduc D. The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity. Biol Chem 2019; 400:629-638. [PMID: 30504522 DOI: 10.1515/hsz-2018-0271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/07/2018] [Indexed: 11/15/2022]
Abstract
Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Indeed, according to the viral eukaryogenesis hypothesis and in light of the endosymbiotic theory, the first eukaryotic cell (our lineage) originated as a consortium consisting of an archaeal ancestor of the eukaryotic cytoplasm, a bacterial ancestor of the mitochondria and a viral ancestor of the nucleus. From a pathologic point of view, the peptide sequence similarity between viruses and humans may provide a molecular platform for autoimmune crossreactions during immune responses following viral infections/immunizations.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, I-70124 Bari, Italy
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13
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A panel of Transcription factors identified by data mining can predict the prognosis of head and neck squamous cell carcinoma. Cancer Cell Int 2019; 19:297. [PMID: 31787845 PMCID: PMC6858662 DOI: 10.1186/s12935-019-1024-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/11/2019] [Indexed: 11/13/2022] Open
Abstract
Background Transcription factors (TFs) are responsible for the regulation of various activities related to cancer like cell proliferation, invasion, and migration. It is thought that, the measurement of TFs levels could assist in developing strategies for diagnosis and prognosis of cancer detection. However, due to lack of effective genome-wide tests, this cannot be carried out in clinical settings. Methods A complete assessment of RNA-seq data in samples of a head and neck squamous cell carcinoma (HNSCC) cohort in The Cancer Genome Atlas (TCGA) database was carried out. From the expression data of six TFs, a risk score model was developed and further validated in the GSE41613 and GSE65858 series. Potential functional roles were identified for the six TFs via gene set enrichment analysis. Results Based on our multi-TF signature, patients are stratified into high- and low-risk groups with significant variations in overall survival (OS) (median survival 2.416 vs. 5.934 years, log-rank test P < 0.001). The sensitivity and specificity evaluation of our multi-TF for 3-year OS in TCGA, GSE41613 and GSE65858 was 0.707, 0.679 and 0.605, respectively, demonstrating good reproducibility and robustness for predicting overall survival of HNSCC patients. Through multivariate Cox regression analyses (MCRA) and stratified analyses, we confirmed that the predictive capability of this risk score (RS) was not dependent on any of other factors like clinicopathological parameters. Conclusions With the help of a RS obtained from a panel of TFs expression signatures, effective OS prediction and stratification of HNSCC patients can be carried out.
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14
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Novel MEIS1-NCOA2 Gene Fusions Define a Distinct Primitive Spindle Cell Sarcoma of the Kidney. Am J Surg Pathol 2019; 42:1562-1570. [PMID: 30179902 DOI: 10.1097/pas.0000000000001140] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We describe 2 cases of a distinct sarcoma characterized by a novel MEIS1-NCOA2 gene fusion. This gene fusion was identified in the renal neoplasms of 2 adults (21-y-old male, 72-y-old female). Histologically, the resected renal neoplasms had a distinctively nodular appearance, and while one renal neoplasm was predominantly cystic, the other demonstrated solid architecture, invasion of perirenal fat, and renal sinus vasculature invasion. The neoplasms were characterized predominantly by monomorphic plump spindle cells arranged in vague fascicles with a whorling pattern; however, a more primitive small round cell component was also noted. Both neoplasms were mitotically active and one case showed necrosis. The neoplasms did not have a distinctive immunohistochemical profile, though both labeled for TLE1. The morphologic features are distinct from other sarcomas associated with NCOA2 gene fusions, including mesenchymal chondrosarcoma, congenital/infantile spindle cell rhabdomyosarcoma, and soft tissue angiofibroma. While we have minimal clinical follow-up, the aggressive histologic features of these neoplasms indicate malignant potential, thus warranting classification as a novel subtype of sarcoma.
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15
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Zhang H, Cheng J, Li Z, Xi Y. Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement. PeerJ 2019; 7:e7628. [PMID: 31523525 PMCID: PMC6717502 DOI: 10.7717/peerj.7628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/06/2019] [Indexed: 12/17/2022] Open
Abstract
Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Zijian Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yaming Xi
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
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16
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Lai CK, Norddahl GL, Maetzig T, Rosten P, Lohr T, Sanchez Milde L, von Krosigk N, Docking TR, Heuser M, Karsan A, Humphries RK. Meis2 as a critical player in MN1-induced leukemia. Blood Cancer J 2017; 7:e613. [PMID: 28960191 PMCID: PMC5709755 DOI: 10.1038/bcj.2017.86] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023] Open
Abstract
Meningioma 1 (MN1) is an independent prognostic marker for normal karyotype acute myeloid leukemia (AML), with high expression linked to all-trans retinoic acid resistance and poor survival. MN1 is also a potent and sufficient oncogene in murine leukemia models, strongly dependent on the MEIS1/AbdB-like HOX protein complex to transform common myeloid progenitors, block myeloid differentiation, and promote leukemic stem cell self-renewal. To identify key genes and pathways underlying leukemic activity, we functionally assessed MN1 cell phenotypic heterogeneity, revealing leukemic and non-leukemic subsets. Using gene expression profiling of these subsets combined with previously published comparisons of full-length MN1 and mutants with varying leukemogenic activity, we identified candidate genes critical to leukemia. Functional analysis identified Hlf and Hoxa9 as critical to MN1 in vitro proliferation, self-renewal and impaired myeloid differentiation. Although critical to transformation, Meis1 knockdown had little impact on these properties in vitro. However, we identified Meis2 as critical to MN1-induced leukemia, with essential roles in proliferation, self-renewal, impairment of differentiation and disease progression in vitro and in vivo. Here, we provide evidence of phenotypic and functional hierarchy in MN1-induced leukemic cells, characterise contributions of Hlf, Hoxa9 and Meis1 to in vitro leukemic properties, and reveal Meis2 as a novel player in MN1-induced leukemogenesis.
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Affiliation(s)
- C K Lai
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - G L Norddahl
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - T Maetzig
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada.,Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - P Rosten
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - T Lohr
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - L Sanchez Milde
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - N von Krosigk
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - T R Docking
- Genome Sciences Centre, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada
| | - M Heuser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - A Karsan
- Genome Sciences Centre, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R K Humphries
- Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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17
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Blasi F, Bruckmann C, Penkov D, Dardaei L. A tale of TALE, PREP1, PBX1, and MEIS1: Interconnections and competition in cancer. Bioessays 2017; 39. [DOI: 10.1002/bies.201600245] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Francesco Blasi
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology; Milan Italy
| | - Chiara Bruckmann
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology; Milan Italy
| | - Dmitry Penkov
- IFOM, Foundation FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology; Milan Italy
| | - Leila Dardaei
- Massachusetts General Hospital Cancer Center; Charlestown MA USA
- Department of Medicine; Harvard Medical School; Boston MA USA
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18
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Cruz-Rodriguez N, Combita AL, Enciso LJ, Raney LF, Pinzon PL, Lozano OC, Campos AM, Peñaloza N, Solano J, Herrera MV, Zabaleta J, Quijano S. Prognostic stratification improvement by integrating ID1/ID3/IGJ gene expression signature and immunophenotypic profile in adult patients with B-ALL. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:37. [PMID: 28245840 PMCID: PMC5331651 DOI: 10.1186/s13046-017-0506-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 02/21/2017] [Indexed: 01/25/2023]
Abstract
Background Survival of adults with B-Acute Lymphoblastic Leukemia requires accurate risk stratification of patients in order to provide the appropriate therapy. Contemporary techniques, using clinical and cytogenetic variables are incomplete for prognosis prediction. Methods To improve the classification of adult patients diagnosed with B-ALL into prognosis groups, two strategies were examined and combined: the expression of the ID1/ID3/IGJ gene signature by RT-PCR and the immunophenotypic profile of 19 markers proposed in the EuroFlow protocol by Flow Cytometry in bone marrow samples. Results Both techniques were correlated to stratify patients into prognostic groups. An inverse relationship between survival and expression of the three-genes signature was observed and an immunophenotypic profile associated with clinical outcome was identified. Markers CD10 and CD20 were correlated with simultaneous overexpression of ID1, ID3 and IGJ. Patients with simultaneous expression of the poor prognosis gene signature and overexpression of CD10 or CD20, had worse Event Free Survival and Overall Survival than patients who had either the poor prognosis gene expression signature or only CD20 or CD10 overexpressed. Conclusion By utilizing the combined evaluation of these two immunophenotypic markers along with the poor prognosis gene expression signature, the risk stratification can be significantly strengthened. Further studies including a large number of patients are needed to confirm these findings. Electronic supplementary material The online version of this article (doi:10.1186/s13046-017-0506-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nataly Cruz-Rodriguez
- Programa de Investigación e Innovación en Leucemias Agudas y Crónicas (PILAC), Instituto Nacional de Cancerología, Bogotá, Colombia.,Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia.,Programa de Doctorado en Ciencias Biológicas, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alba L Combita
- Programa de Investigación e Innovación en Leucemias Agudas y Crónicas (PILAC), Instituto Nacional de Cancerología, Bogotá, Colombia. .,Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia. .,Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Leonardo J Enciso
- Programa de Investigación e Innovación en Leucemias Agudas y Crónicas (PILAC), Instituto Nacional de Cancerología, Bogotá, Colombia.,Grupo de Hemato-Oncología, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Lauren F Raney
- Department of Pediatrics, Pediatric Hematology-Oncology Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Children's Hospital of New Orleans, New Orleans, LA, USA
| | - Paula L Pinzon
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Olga C Lozano
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Alba M Campos
- Hospital Universitario San Ignacio, Bogotá, Colombia
| | | | - Julio Solano
- Hospital Universitario San Ignacio, Bogotá, Colombia
| | | | - Jovanny Zabaleta
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Sandra Quijano
- Hospital Universitario San Ignacio, Bogotá, Colombia. .,Grupo de Inmunobiología y Biología Celular, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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19
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Sharma P, Lin T, Hannapel DJ. Targets of the StBEL5 Transcription Factor Include the FT Ortholog StSP6A. PLANT PHYSIOLOGY 2016; 170:310-24. [PMID: 26553650 PMCID: PMC4704582 DOI: 10.1104/pp.15.01314] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/06/2015] [Indexed: 05/03/2023]
Abstract
The BEL1-like family of transcription factors is ubiquitous in plants and plays important roles in regulating development. They function in tandem with KNOTTED1 types to bind to a double TTGAC motif in the upstream sequence of target genes. StBEL5 of potato (Solanum tuberosum) functions as a mobile RNA signal that is transcribed in leaves, moves down into stolons in response to short days, and induces tuber formation. Despite their importance, however, very little is known about the targets of BEL1-like transcription factors. To better understand this network, we made use of a phloem-mobile BEL5 induction model, an ethanol-inducible system coupled with RNA sequencing analysis, and a screen for tandem TTGAC cis-elements in the upstream sequence to catalog StBEL5 target genes. Induction of StBEL5 activated several genes that are also induced by StSP6A (S. tuberosum SELF-PRUNING 6A), a FLOWERING LOCUS T coregulator that functions as a signal for tuberization. Both enhancement and suppression of StBEL5 expression were also closely linked to StSP6A transcriptional activity. Site mutagenesis in tandem TTGAC motifs located in the upstream sequence of StSP6A suppressed the short day-induced activity of its promoter in both young tubers and leaves. The expression profile of StBEL5 induced in stolons from plants grown under long-day conditions revealed almost 10,000 differentially expressed genes, including important tuber marker genes and genes involved in cell growth, transcription, floral development, and hormone metabolism. In a random screen of 200 differentially expressed targets of StBEL5, 92% contained tandem TTGAC motifs in the upstream sequence within 3 kb of the transcription start site.
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Affiliation(s)
- Pooja Sharma
- Plant Biology Major, Iowa State University, Ames, Iowa 50011-1100
| | - Tian Lin
- Plant Biology Major, Iowa State University, Ames, Iowa 50011-1100
| | - David J Hannapel
- Plant Biology Major, Iowa State University, Ames, Iowa 50011-1100
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20
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Yi SH, Xu LC, Mei K, Yang RZ, Huang DX. Isolation and identification of age-related DNA methylation markers for forensic age-prediction. Forensic Sci Int Genet 2014; 11:117-25. [PMID: 24727429 DOI: 10.1016/j.fsigen.2014.03.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 03/03/2014] [Accepted: 03/12/2014] [Indexed: 12/27/2022]
Abstract
Age-prediction is an important part of forensic science. There is no available method of individual age-prediction for general forensic biological samples at crime scenes. Accumulating evidence indicates that aging resembles a developmentally regulated process tightly controlled by specific age-associated methylation exists in human genome. This study isolated and identified eight gene fragments in which the degree of cytosine methylation is significantly correlated with age in blood of 40 donors. Furthermore, we validated two CpG sites of each gene fragment and replicated our results in a general population sample of 40 males and 25 females with a wide age-range (11-72 years). The methylation of these fragments is linear with age over a range of six decades (Fragment P1 (r=-0.64), P2 (r=-0.58), P3 (r=-0.79), R1 (r=0.82), R2 (r=0.63), R3 (r=0.59), R4 (r=0.63) and R5 (r=0.62)). Using average methylation of two CpG sites from each fragment, we built a regression model that explained 95% of the variance in age and is able to predict the age of an individual with great accuracy (R(2)=0.918). The predicted values are highly correlated with the observed age in the sample (r=0.91). This study implicates that DNA methylation will be an available biological marker of age-prediction. Furthermore, measurement of relevant sites in the genome could be a tool in routine forensic screening to predict age of biological samples.
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Affiliation(s)
- Shao Hua Yi
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Long Chang Xu
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Kun Mei
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Rong Zhi Yang
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Dai Xin Huang
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China.
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Abstract
TG-interacting factor 1 (TGIF1) is a transcriptional repressor that can modulate retinoic acid and transforming growth factor β signaling pathways. It is required for myeloid progenitor cell differentiation and survival, and mutations in the TGIF1 gene cause holoprosencephaly. Furthermore, we have previously observed that acute myelogenous leukemia (AML) patients with low TGIF1 levels had worse prognoses. Here, we explored the role of Tgif1 in murine hematopoietic stem cell (HSC) function. CFU assays showed that Tgif1(-/-) bone marrow cells produced more total colonies and had higher serial CFU potential. These effects were also observed in vivo, where Tgif1(-/-) bone marrow cells had higher repopulation potential in short- and long-term competitive repopulation assays than wild-type cells. Serial transplantation and replating studies showed that Tgif1(-/-) HSCs exhibited greater self-renewal and were less proliferative and more quiescent than wild-type cells, suggesting that Tgif1 is required for stem cells to enter the cell cycle. Furthermore, HSCs from Tgif1(+/-) mice had a phenotype similar to that of HSCs from Tgif1(-/-) mice, while bone marrow cells with overexpressing Tgif1 showed increased proliferation and lower survival in long-term transplant studies. Taken together, our data suggest that Tgif1 suppresses stem cell self-renewal and provide clues as to how reduced expression of TGIF1 may contribute to poor long-term survival in patients with AML.
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22
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Liu Z, Gao F, Hou L, Qian Y, Tian R. Network clusters analysis based on protein-protein interaction network constructed in phosgene-induced acute lung injury. Lung 2013; 191:545-51. [PMID: 23963411 DOI: 10.1007/s00408-013-9493-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/25/2013] [Indexed: 11/27/2022]
Abstract
PURPOSE Acute lung injury (ALI) is characterized by impairment in gas exchange and/or lung mechanics that leads to hypoxemia with the presence of diffuse pulmonary infiltrate. Assessments of lung injury play important roles in the development of rational medical countermeasures. The purpose of this study is to investigate the molecular mechanisms of phosgene-induced lung injury. METHODS We downloaded the gene expression profile of lung tissue from mice exposed to air or phosgene from gene expression omnibus database and identified differentially expressed genes (DEGs) in ALI. Furthermore, we constructed a protein-protein interaction (PPI) network and identified network clusters. RESULTS In total, 582 DEGs were found and 4 network clusters were identified in the constructed PPI network. Gene set enrichment analysis found that DEGs were mainly involved in mitochondrion organization and biogenesis, mRNA metabolic process, negative regulation of transferase activity or catalytic activity, and coenzyme metabolic process. Pathways of spliceosome, glutathione metabolism, and cell cycle were dysregulated in phosgene-induced ALI. Besides, we identified four genes, including F3, Meis1, Pvf, and Cdc6 in network clusters, which may be used as biomarkers of phosgene-induced ALI. CONCLUSIONS Our results revealed biological processes and pathways involved in phosgene-induced ALI and may expand understandings of phosgene-induced ALI. However, further experiments are needed to confirm our findings.
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Affiliation(s)
- Zhenwei Liu
- Department of Respiratory Medicine, First People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200080, China
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23
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Chen L, Stuart L, Ohsumi TK, Burgess S, Varshney GK, Dastur A, Borowsky M, Benes C, Lacy-Hulbert A, Schmidt EV. Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics. BMC Cancer 2013; 13:93. [PMID: 23442791 PMCID: PMC3598783 DOI: 10.1186/1471-2407-13-93] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/19/2013] [Indexed: 11/16/2022] Open
Abstract
Background The development of resistance to chemotherapies represents a significant barrier to successful cancer treatment. Resistance mechanisms are complex, can involve diverse and often unexpected cellular processes, and can vary with both the underlying genetic lesion and the origin or type of tumor. For these reasons developing experimental strategies that could be used to understand, identify and predict mechanisms of resistance in different malignant cells would be a major advance. Methods Here we describe a gain-of-function forward genetic approach for identifying mechanisms of resistance. This approach uses a modified piggyBac transposon to generate libraries of mutagenized cells, each containing transposon insertions that randomly activate nearby gene expression. Genes of interest are identified using next-gen high-throughput sequencing and barcode multiplexing is used to reduce experimental cost. Results Using this approach we successfully identify genes involved in paclitaxel resistance in a variety of cancer cell lines, including the multidrug transporter ABCB1, a previously identified major paclitaxel resistance gene. Analysis of co-occurring transposons integration sites in single cell clone allows for the identification of genes that might act cooperatively to produce drug resistance a level of information not accessible using RNAi or ORF expression screening approaches. Conclusion We have developed a powerful pipeline to systematically discover drug resistance in mammalian cells in vitro. This cost-effective approach can be readily applied to different cell lines, to identify canonical or context specific resistance mechanisms. Its ability to probe complex genetic context and non-coding genomic elements as well as cooperative resistance events makes it a good complement to RNAi or ORF expression based screens.
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Affiliation(s)
- Li Chen
- Center for Molecular Therapeutics, Center for Cancer Research, Massachusetts General Hospital, and Harvard Medical School, CNY 149-Rm7308, Thirteenth St. Charlestown, MA 02129, USA.
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Bruserud O, Reikvam H, Kittang AO, Ahmed AB, Tvedt THA, Sjo M, Hatfield KJ. High-dose etoposide in allogeneic stem cell transplantation. Cancer Chemother Pharmacol 2012; 70:765-82. [PMID: 23053272 DOI: 10.1007/s00280-012-1990-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/19/2012] [Indexed: 12/19/2022]
Abstract
The anti-leukemic effect of etoposide is well documented. High-dose etoposide 60 mg/kg in combination with fractionated total body irradiation (TBI), usually single fractions of 1.2 Gy up to a total of 13.2 Gy, is used as conditioning therapy for allogeneic stem cell transplantation. Most studies of this conditioning regimen have included patients with acute leukemia receiving bone marrow or mobilized stem cell grafts derived from family or matched unrelated donors, and the treatment is then effective even in patients with high-risk disease. The most common adverse effects are fever with hypotension and rash, nausea and vomiting, sialoadenitis, neuropathy and metabolic acidosis. A small minority of patients develop severe allergic reactions. Etoposide has also been tested in a wide range of combination regimens, but for many of these combinations, relatively few patients are included, and some combinations have only been tested in patients who have undergone autologous transplants. However, the general conclusion is that many of these combinations are effective in patients with high-risk malignancies and the toxicity often seems acceptable. Thus, etoposide-based conditioning therapy should be further evaluated in patients having allogeneic transplants, but randomized trials are needed and the design of future trials should be based on the well-characterized TBI + high-dose etoposide regimen.
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Affiliation(s)
- Oystein Bruserud
- Department of Medicine, Section of Hematology, Haukeland University Hospital, Bergen, Norway
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