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Griffen TL, Dammer EB, Dill CD, Carey KM, Young CD, Nunez SK, Ohandjo AQ, Kornblau SM, Lillard JW. Multivariate transcriptome analysis identifies networks and key drivers of chronic lymphocytic leukemia relapse risk and patient survival. BMC Med Genomics 2021; 14:171. [PMID: 34187466 PMCID: PMC8243588 DOI: 10.1186/s12920-021-01012-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/10/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Chronic lymphocytic leukemia (CLL) is an indolent heme malignancy characterized by the accumulation of CD5+ CD19+ B cells and episodes of relapse. The biological signaling that influence episodes of relapse in CLL are not fully described. Here, we identify gene networks associated with CLL relapse and survival risk. METHODS Networks were investigated by using a novel weighted gene network co-expression analysis method and examining overrepresentation of upstream regulators and signaling pathways within co-expressed transcriptome modules across clinically annotated transcriptomes from CLL patients (N = 203). Gene Ontology analysis was used to identify biological functions overrepresented in each module. Differential Expression of modules and individual genes was assessed using an ANOVA (Binet Stage A and B relapsed patients) or T-test (SF3B1 mutations). The clinical relevance of biomarker candidates was evaluated using log-rank Kaplan Meier (survival and relapse interval) and ROC tests. RESULTS Eight distinct modules (M2, M3, M4, M7, M9, M10, M11, M13) were significantly correlated with relapse and differentially expressed between relapsed and non-relapsed Binet Stage A CLL patients. The biological functions of modules positively correlated with relapse were carbohydrate and mRNA metabolism, whereas negatively correlated modules to relapse were protein translation associated. Additionally, M1, M3, M7, and M13 modules negatively correlated with overall survival. CLL biomarkers BTK, BCL2, and TP53 were co-expressed, while unmutated IGHV biomarker ZAP70 and cell survival-associated NOTCH1 were co-expressed in modules positively correlated with relapse and negatively correlated with survival days. CONCLUSIONS This study provides novel insights into CLL relapse biology and pathways associated with known and novel biomarkers for relapse and overall survival. The modules associated with relapse and overall survival represented both known and novel pathways associated with CLL pathogenesis and can be a resource for the CLL research community. The hub genes of these modules, e.g., ARHGAP27P2, C1S, CASC2, CLEC3B, CRY1, CXCR5, FUT5, MID1IP1, and URAHP, can be studied further as new therapeutic targets or clinical markers to predict CLL patient outcomes.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Gene Expression Profiling
- Gene Regulatory Networks
- Male
- Female
- Recurrence
- Multivariate Analysis
- Biomarkers, Tumor/genetics
- Middle Aged
- Transcriptome
- Aged
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Prognosis
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Affiliation(s)
- Ti'ara L Griffen
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, 720 Westview Dr SW, HG 341B, Atlanta, GA, 30310, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Courtney D Dill
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, 720 Westview Dr SW, HG 341B, Atlanta, GA, 30310, USA
| | - Kaylin M Carey
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, 720 Westview Dr SW, HG 341B, Atlanta, GA, 30310, USA
| | - Corey D Young
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, 720 Westview Dr SW, HG 341B, Atlanta, GA, 30310, USA
| | - Sha'Kayla K Nunez
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, 720 Westview Dr SW, HG 341B, Atlanta, GA, 30310, USA
| | - Adaugo Q Ohandjo
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, 720 Westview Dr SW, HG 341B, Atlanta, GA, 30310, USA
| | - Steven M Kornblau
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - James W Lillard
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, 720 Westview Dr SW, HG 341B, Atlanta, GA, 30310, USA.
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Wieland L, Engel K, Volkmer I, Krüger A, Posern G, Kornhuber ME, Staege MS, Emmer A. Overexpression of Endogenous Retroviruses and Malignancy Markers in Neuroblastoma Cell Lines by Medium-Induced Microenvironmental Changes. Front Oncol 2021; 11:637522. [PMID: 34026614 PMCID: PMC8138558 DOI: 10.3389/fonc.2021.637522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/09/2021] [Indexed: 12/21/2022] Open
Abstract
Neuroblastoma (NB) is the commonest solid tumor outside the central nervous system in infancy and childhood with a unique biological heterogeneity. In patients with advanced, metastasizing neuroblastoma, treatment failure and poor prognosis is often marked by resistance to chemo- or immunotherapy. Thus, identification of robust biomarkers seems essential for understanding tumor progression and developing effective therapy. Here, we have studied the expression of human endogenous retroviruses (HERV) as potential targets in NB cell lines during stem-cell medium-induced microenvironmental change. Quantitative PCR revealed that relative expression of the HERV-K family and HERV-W1 ENV were increased in all three NB cell lines after incubation in stem-cell medium. Virus transcriptome analyses revealed the transcriptional activation of three endogenous retrovirus elements: HERV-R ENV (ERV3-1), HERV-E1 and HERV-Fc2 ENV (ERVFC1-1). Known malignancy markers in NB, e.g. proto-oncogenic MYC or MYCN were expressed highly heterogeneously in the three investigated NB cell lines with up-regulation of MYC and MYCN upon medium-induced microenvironmental change. In addition, SiMa cells exclusively showed a phenotype switching from loosely-adherent monolayers to low proliferating grape-like cellular aggregates, which was accompanied by an enhanced CD133 expression. Interestingly, the overexpression of HERV was associated with a significant elevation of immune checkpoint molecule CD200 in both quantitative PCR and RNA-seq analysis suggesting tumor escape mechanism in NB cell lines after incubation in serum-free stem cell medium.
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Affiliation(s)
- Lisa Wieland
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany.,Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Kristina Engel
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ines Volkmer
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Anna Krüger
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Guido Posern
- Institute for Physiological Chemistry, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Malte E Kornhuber
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin S Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Alexander Emmer
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
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Zhang N, Zhang S, Wu W, Lu W, Jiang M, Zheng N, Huang J, Wang L, Liu H, Zheng M, Wang J. Regorafenib inhibits migration, invasion, and vasculogenic mimicry of hepatocellular carcinoma via targeting ID1-mediated EMT. Mol Carcinog 2021; 60:151-163. [PMID: 33428809 DOI: 10.1002/mc.23279] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/20/2022]
Abstract
Regorafenib is approved for patients with unresectable hepatocellular carcinoma (HCC) following sorafenib. However, the effect of regorafenib on HCC metastasis and its mechanism are poorly understood. Here, our data showed that regorafenib significantly restrained the migration, invasion and vasculogenic mimicry (VM) of HCC cells, and downregulated the expression of epithelial-to-mesenchymal transition (EMT)/VM-related molecules. Using RNA-seq and cellular thermal shift assays, we found that inhibitor of differentiation 1 (ID1) was a key target of regorafenib. In HCC tissues, the protein expression of ID1 was positively correlated with EMT and VM formation (CD34- /PAS+ ). Functionally, ID1 knockdown inhibited HCC cell migration, invasion, metastasis, and VM formation in vitro and in vivo, with upregulation of E-cadherin and downregulation of Snail and VE-cadherin. Moreover, Snail overexpression promoted the migration, invasion, and VM formation of ID1 knockdown cells. Snail knockdown reduced the migration, invasion, and VM formation of ID1 overexpression cells. Finally, regorafenib suppressed VM formation and decreased the expression of ID1, VE-cadherin and Snail in HCC PDX model. In conclusion, we manifested that regorafenib distinctly inhibited EMT in HCC cells via targeting ID1, leading to the suppression of cell migration, invasion and VM formation. These findings suggest that regorafenib may be developed as a suitable therapeutic agent for HCC metastasis.
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Affiliation(s)
- Nan Zhang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Shaoqin Zhang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Wenda Wu
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Wenxian Lu
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Mingting Jiang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Ning Zheng
- Department of Pharmacology, Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, The School of Pharmacy, Fujian Medical University, Fujian, China
| | - Jing Huang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Long Wang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Hekun Liu
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Min Zheng
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
| | - Jichuang Wang
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, The School of Basic Medical Sciences, Fujian Medical University, Fujian, China
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Kuang X, Xiong J, Lu T, Wang W, Zhang Z, Wang J. Inhibition of USP1 induces apoptosis via ID1/AKT pathway in B-cell acute lymphoblastic leukemia cells. Int J Med Sci 2021; 18:245-255. [PMID: 33390793 PMCID: PMC7738972 DOI: 10.7150/ijms.47597] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
Deubiquitylating enzyme ubiquitin-specific protease 1 (USP1) has been reported to be aberrantly overexpressed in cancers, and it plays a critical role in regulating various cellular processes, such as cell proliferation, apoptosis, and cell differentiation. However, the role of USP1 in B-cell acute lymphoblastic leukemia (B-ALL) remains largely undefined. USP1 expression in 30 newly diagnosed B-ALL patients was detected by real-time PCR and western blot. We found that USP1 was generally upregulated in the bone marrow cells derived from B-ALL patients. Knockdown of USP1 by siRNA decreased B-ALL cell growth and induced apoptosis. Similarly, pharmacological inhibition of USP1 by SJB3-019A significantly repressed cell proliferation and triggered B-ALL cell apoptosis. Finally, we found that inhibition of USP1 downregulated the expression of ID1 and p-AKT, and upregulated ID1 expression could reverse the suppressive effects of USP1 inhibitor in B-ALL cells. Taken together, these results demonstrate that USP1 promote B-ALL progression at least partially via the ID1/AKT signaling pathway, and USP1 inhibitors might be promising therapeutic application for B-ALL.
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Affiliation(s)
- Xingyi Kuang
- Department of Hematology, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, P.R. China.,Guizhou Province Hematopoietic Stem Cell Transplantation Center, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, P.R. China.,Key Laboratory of Hematological Disease Diagnostic & Treat Centre of Guizhou Province, Guiyang 550004, P.R. China.,School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, P.R. China
| | - Jie Xiong
- Department of Hematology, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, P.R. China.,Guizhou Province Hematopoietic Stem Cell Transplantation Center, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, P.R. China.,Key Laboratory of Hematological Disease Diagnostic & Treat Centre of Guizhou Province, Guiyang 550004, P.R. China
| | - Tingting Lu
- Key Laboratory of Hematological Disease Diagnostic & Treat Centre of Guizhou Province, Guiyang 550004, P.R. China
| | - Weili Wang
- Key Laboratory of Hematological Disease Diagnostic & Treat Centre of Guizhou Province, Guiyang 550004, P.R. China
| | - Zhaoyuan Zhang
- Key Laboratory of Hematological Disease Diagnostic & Treat Centre of Guizhou Province, Guiyang 550004, P.R. China
| | - Jishi Wang
- Department of Hematology, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, P.R. China.,Guizhou Province Hematopoietic Stem Cell Transplantation Center, The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, P.R. China.,Key Laboratory of Hematological Disease Diagnostic & Treat Centre of Guizhou Province, Guiyang 550004, P.R. China
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