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Binder M, Szalat RE, Talluri S, Fulciniti M, Avet-Loiseau H, Parmigiani G, Samur MK, Munshi NC. Bone marrow stromal cells induce chromatin remodeling in multiple myeloma cells leading to transcriptional changes. Nat Commun 2024; 15:4139. [PMID: 38755155 PMCID: PMC11098817 DOI: 10.1038/s41467-024-47793-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
The natural history of multiple myeloma is characterized by its localization to the bone marrow and its interaction with bone marrow stromal cells. The bone marrow stromal cells provide growth and survival signals, thereby promoting the development of drug resistance. Here, we show that the interaction between bone marrow stromal cells and myeloma cells (using human cell lines) induces chromatin remodeling of cis-regulatory elements and is associated with changes in the expression of genes involved in the cell migration and cytokine signaling. The expression of genes involved in these stromal interactions are observed in extramedullary disease in patients with myeloma and provides the rationale for survival of myeloma cells outside of the bone marrow microenvironment. Expression of these stromal interaction genes is also observed in a subset of patients with newly diagnosed myeloma and are akin to the transcriptional program of extramedullary disease. The presence of such adverse stromal interactions in newly diagnosed myeloma is associated with accelerated disease dissemination, predicts the early development of therapeutic resistance, and is of independent prognostic significance. These stromal cell induced transcriptomic and epigenomic changes both predict long-term outcomes and identify therapeutic targets in the tumor microenvironment for the development of novel therapeutic approaches.
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Affiliation(s)
- Moritz Binder
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Srikanth Talluri
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | | | - Hervé Avet-Loiseau
- University Cancer Center of Toulouse, Institut National de la Santé, Toulouse, France
| | - Giovanni Parmigiani
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mehmet K Samur
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
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2
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Chen W, Hong SH, Jenks SA, Anam FA, Tipton CM, Woodruff MC, Hom JR, Cashman KS, Faliti CE, Wang X, Kyu S, Wei C, Scharer CD, Mi T, Hicks S, Hartson L, Nguyen DC, Khosroshahi A, Lee S, Wang Y, Bugrovsky R, Ishii Y, Lee FEH, Sanz I. Distinct transcriptomes and autocrine cytokines underpin maturation and survival of antibody-secreting cells in systemic lupus erythematosus. Nat Commun 2024; 15:1899. [PMID: 38429276 PMCID: PMC10907730 DOI: 10.1038/s41467-024-46053-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/09/2024] [Indexed: 03/03/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multiple autoantibody types, some of which are produced by long-lived plasma cells (LLPC). Active SLE generates increased circulating antibody-secreting cells (ASC). Here, we examine the phenotypic, molecular, structural, and functional features of ASC in SLE. Relative to post-vaccination ASC in healthy controls, circulating blood ASC from patients with active SLE are enriched with newly generated mature CD19-CD138+ ASC, similar to bone marrow LLPC. ASC from patients with SLE displayed morphological features of premature maturation and a transcriptome epigenetically initiated in SLE B cells. ASC from patients with SLE exhibited elevated protein levels of CXCR4, CXCR3 and CD138, along with molecular programs that promote survival. Furthermore, they demonstrate autocrine production of APRIL and IL-10, which contributed to their prolonged in vitro survival. Our work provides insight into the mechanisms of generation, expansion, maturation and survival of SLE ASC.
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Affiliation(s)
- Weirong Chen
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - So-Hee Hong
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
- Department of Microbiology, Ewha Womans University, Seoul, Republic of Korea
| | - Scott A Jenks
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Fabliha A Anam
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher M Tipton
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jennifer R Hom
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kevin S Cashman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Caterina Elisa Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Xiaoqian Wang
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Shuya Kyu
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Chungwen Wei
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Tian Mi
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Sakeenah Hicks
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Louise Hartson
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Doan C Nguyen
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Arezou Khosroshahi
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Saeyun Lee
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Youliang Wang
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Regina Bugrovsky
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yusho Ishii
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - F Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, School of Medicine, Emory University, Atlanta, GA, USA.
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3
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Gong TT, Liu FH, Xiao Q, Li YZ, Wei YF, Xu HL, Cao F, Sun ML, Jiang FL, Tao T, Ma QP, Qin X, Song Y, Gao S, Wu L, Zhao YH, Huang DH, Wu QJ. SH3RF2 contributes to cisplatin resistance in ovarian cancer cells by promoting RBPMS degradation. Commun Biol 2024; 7:67. [PMID: 38195842 PMCID: PMC10776562 DOI: 10.1038/s42003-023-05721-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024] Open
Abstract
Platinum-based chemotherapy remains one of the major choices for treatment of ovarian cancer (OC). However, primary or acquired drug resistance severely impairs their efficiency, thereby causing chemotherapy failure and poor prognosis. SH3 domain containing ring finger 2 (SH3RF2) has been linked to the development of cancer. Here we find higher levels of SH3RF2 in the tumor tissues from cisplatin-resistant OC patients when compared to those from cisplatin-sensitive patients. Similarly, cisplatin-resistant OC cells also express higher levels of SH3RF2 than normal OC cells. Through in vitro and in vivo loss-of-function experiments, SH3RF2 is identified as a driver of cisplatin resistance, as evidenced by increases in cisplatin-induced cell apoptosis and DNA damage and decreases in cell proliferation induced by SH3RF2 depletion. Mechanistically, SH3RF2 can directly bind to the RNA-binding protein mRNA processing factor (RBPMS). RBPMS has been reported as an inhibitor of cisplatin resistance in OC. As a E3 ligase, SH3RF2 promotes the K48-linked ubiquitination of RBPMS to increase its proteasomal degradation and activator protein 1 (AP-1) transactivation. Impairments in RBPMS function reverse the inhibitory effect of SH3RF2 depletion on cisplatin resistance. Collectively, the SH3RF2-RBPMS-AP-1 axis is an important regulator in cisplatin resistance and inhibition of SH3RF2 may be a potential target in preventing cisplatin resistance.
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Affiliation(s)
- Ting-Ting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fang-Hua Liu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qian Xiao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yi-Zi Li
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yi-Fan Wei
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - He-Li Xu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fan Cao
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ming-Li Sun
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Feng-Li Jiang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tao Tao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qi-Peng Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xue Qin
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.
| | - Yang Song
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Song Gao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lang Wu
- Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Yu-Hong Zhao
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China
| | - Dong-Hui Huang
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China.
- Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China.
| | - Qi-Jun Wu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China.
- Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China.
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China.
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4
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Liu H, Fu H, Yu C, Zhang N, Huang C, Lv L, Hu C, Chen F, Xiao Z, Zhang Z, Lu H, Yuan K. Transcriptional pausing induced by ionizing radiation enables the acquisition of radioresistance in nasopharyngeal carcinoma. J Mol Cell Biol 2024; 15:mjad044. [PMID: 37407287 PMCID: PMC10960568 DOI: 10.1093/jmcb/mjad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/24/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Lesions on the DNA template can impact transcription via distinct regulatory pathways. Ionizing radiation (IR) as the mainstay modality for many malignancies elicits most of the cytotoxicity by inducing a variety of DNA damages in the genome. How the IR treatment alters the transcription cycle and whether it contributes to the development of radioresistance remain poorly understood. Here, we report an increase in the paused RNA polymerase II (RNAPII), as indicated by the phosphorylation at serine 5 residue of its C-terminal domain, in recurrent nasopharyngeal carcinoma (NPC) patient samples after IR treatment and cultured NPC cells developing IR resistance. Reducing the pool of paused RNAPII by either inhibiting TFIIH-associated CDK7 or stimulating the positive transcription elongation factor b, a CDK9-CycT1 heterodimer, attenuates IR resistance of NPC cells. Interestingly, the poly(ADP-ribosyl)ation of CycT1, which disrupts its phase separation, is elevated in the IR-resistant cells. Mutation of the major poly(ADP-ribosyl)ation sites of CycT1 decreases RNAPII pausing and restores IR sensitivity. Genome-wide chromatin immunoprecipitation followed by sequencing analyses reveal that several genes involved in radiation response and cell cycle control are subject to the regulation imposed by the paused RNAPII. Particularly, we identify the NIMA-related kinase NEK7 under such regulation as a new radioresistance factor, whose downregulation results in the increased chromosome instability, enabling the development of IR resistance. Overall, our results highlight a novel link between the alteration in the transcription cycle and the acquisition of IR resistance, opening up new opportunities to increase the efficacy of radiotherapy and thwart radioresistance in NPC.
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Affiliation(s)
- Honglu Liu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huanyi Fu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chunhong Yu
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Na Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Canhua Huang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lu Lv
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Chunhong Hu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Fang Chen
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Zhiqiang Xiao
- Research Center of Carcinogenesis and Targeted Therapy, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhuohua Zhang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- The Biobank of Xiangya Hospital, Central South University, Changsha 410008, China
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5
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Li S, Wei Y, Sun X, Liu M, Zhu M, Yuan Y, Zhang J, Dong Y, Hu K, Ma S, Zhang X, Xu B, Jiang H, Gan L, Liu T. JUNB mediates oxaliplatin resistance via the MAPK signaling pathway in gastric cancer by chromatin accessibility and transcriptomic analysis. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1784-1796. [PMID: 37337631 PMCID: PMC10679881 DOI: 10.3724/abbs.2023119] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/19/2023] [Indexed: 06/21/2023] Open
Abstract
Currently, platinum-containing regimens are the most commonly used regimens for advanced gastric cancer patients, and chemotherapy resistance is one of the main reasons for treatment failure. Thus, it is important to reveal the mechanism of oxaliplatin resistance and to seek effective intervention strategies to improve chemotherapy sensitivity, thereby improving the survival and prognosis of gastric cancer patients. To understand the molecular mechanisms of oxaliplatin resistance, we generate an oxaliplatin-resistant gastric cancer cell line and conduct assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) for both parental and oxaliplatin-resistant AGS cells. A total of 3232 genomic regions are identified to have higher accessibility in oxaliplatin-resistant cells, and DNA-binding motif analysis identifies JUNB as the core transcription factor in the regulatory network. JUNB is overexpressed in oxaliplatin-resistant gastric cancer cells, and its upregulation is associated with poor prognosis in gastric cancer patients, which is validated by our tissue microarray data. Moreover, chromatin immunoprecipitation sequencing (ChIP-seq) analysis reveals that JUNB binds to the transcriptional start site of key genes involved in the MAPK signaling pathway. Knockdown of JUNB inhibits the MAPK signaling pathway and restores sensitivity to oxaliplatin. Combined treatment with the ERK inhibitor piperlongumine or MEK inhibitor trametinib effectively overcomes oxaliplatin resistance. This study provides evidence that JUNB mediates oxaliplatin resistance in gastric cancer by activating the MAPK pathway. The combination of MAPK inhibitors with oxaliplatin overcomes resistance to oxaliplatin, providing a promising treatment opportunity for oxaliplatin-resistant gastric cancer patients.
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Affiliation(s)
- Suyao Li
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Yichou Wei
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Xun Sun
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Mengling Liu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Mengxuan Zhu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Yitao Yuan
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Jiayu Zhang
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Yu Dong
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Keshu Hu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Sining Ma
- Department of Obstetrics and GynecologyZhongshan HospitalShanghai200032China
| | - Xiuping Zhang
- Department of OncologyZhongshan Hospital (Xiamen)Fudan UniversityXiamen361004China
| | - Bei Xu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
- Cancer CenterZhongshan HospitalFudan UniversityShanghai200032China
| | - Hesheng Jiang
- Department of SurgerySouthwest HealthcareSouthern California Medical Education ConsortiumTemecula Valley HospitalTemeculaCA92592USA
| | - Lu Gan
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
- Cancer CenterZhongshan HospitalFudan UniversityShanghai200032China
| | - Tianshu Liu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
- Cancer CenterZhongshan HospitalFudan UniversityShanghai200032China
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6
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Zhang Z, Shi J, Wu Q, Zhang Z, Liu X, Ren A, Zhao G, Dong G, Wu H, Zhao J, Zhao Y, Hu J, Li H, Zhang T, Zhou F, Zhu H. JUN mediates glucocorticoid resistance by stabilizing HIF1a in T cell acute lymphoblastic leukemia. iScience 2023; 26:108242. [PMID: 38026210 PMCID: PMC10661119 DOI: 10.1016/j.isci.2023.108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/23/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Dexamethasone (Dex) plays a critical role in T-ALL treatment, but the mechanisms of Dex resistance are poorly understood. Here, we demonstrated that the expression of JUN was regulated in Dex-resistant T-ALL cell lines and patient samples. JUN knockdown increased the sensitivity to Dex. Moreover, the survival data showed that high expression of JUN related to poor prognosis of T-ALL patients. Then, we generated dexamethasone-resistant clones and conducted RNA-seq and ATAC-seq. We demonstrated that the upregulation of JUN was most significant and regulated by JNK pathway in Dex-resistant cells. High-throughput screening showed that HIF1α inhibitors synergized with Dex could enhance Dex resistance cells death in vitro and in vivo. Additionally, JUN combined and stabilized HIF1α in Dex resistance cells. These results reveal a new mechanism of Dex resistance in T-ALL and provide experimental evidence for the potential therapeutic benefit of targeting the JNK-JUN-HIF1α axis for T-ALL treatment.
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Affiliation(s)
- Zhijie Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Jiangzhou Shi
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Qifang Wu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Zijian Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Xiaoyan Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Anqi Ren
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Guanlin Zhao
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Ge Dong
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Han Wu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Jiaxuan Zhao
- Key Lab of Industrial Fermentation Microbiology of the Ministry of Education & Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuan Zhao
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Jia Hu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Hui Li
- Tianyou Hospital affiliated to Wuhan University of Science and Technology, Wuhan 430064, China
| | - Tongcun Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
- Key Lab of Industrial Fermentation Microbiology of the Ministry of Education & Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Haichuan Zhu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan 430081, China
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7
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Liang T, Tao T, Wu K, Liu L, Xu W, Zhou D, Fang H, Ding Q, Huang G, Wu S. Cancer-Associated Fibroblast-Induced Remodeling of Tumor Microenvironment in Recurrent Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303230. [PMID: 37743226 PMCID: PMC10625065 DOI: 10.1002/advs.202303230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/24/2023] [Indexed: 09/26/2023]
Abstract
Bladder carcinoma (BC) recurrence is a major clinical challenge, and targeting the tumor microenvironment (TME) is a promising therapy. However, the relationship between individual TME components, particularly cancer-associated fibroblasts (CAFs), and tumor recurrence is unclear. Here, TME heterogeneity in primary and recurrent BC is investigated using single-cell RNA sequence profiling of 62 460 cells. Two cancer stem cell (CSC) subtypes are identified in recurrent BC. An inflammatory CAF subtype, ICAM1+ iCAFs, specifically associated with BC recurrence is also identified. iCAFs are found to secrete FGF2, which acts on the CD44 receptor of rCSC-M, thereby maintaining tumor stemness and epithelial-mesenchymal transition. Additionally, THBS1+ monocytes, a group of myeloid-derived suppressor cells (MDSCs), are enriched in recurrent BC and interacted with CAFs. ICAM1+ iCAFs are found to secrete CCL2, which binds to CCR2 in MDSCs. Moreover, elevated STAT3, NFKB2, VEGFA, and CTGF levels in iCAFs reshape the TME in recurrent tumors. CCL2 inhibition in an in situ BC mouse model suppressed tumor growth, decreased MDSCs and Tregs, and fostered tumor immune suppression. The study results highlight the role of iCAFs in TME cell-cell crosstalk during recurrent BC. The identification of pivotal signaling factors driving BC relapse is promising for the development of novel therapies.
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Affiliation(s)
- Ting Liang
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Tao Tao
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Kai Wu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Lisha Liu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Wuwu Xu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Dewang Zhou
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Hu Fang
- Department of UrologySouth China Hospital of Shenzhen UniversityShenzhen518000China
| | - Qiuxia Ding
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Guixiao Huang
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
| | - Song Wu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
- Department of UrologySouth China Hospital of Shenzhen UniversityShenzhen518000China
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8
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Tang S, Zhang F, Li J, Dong H, Yang Q, Liu J, Fu Y. The selective activator protein-1 inhibitor T-5224 regulates the IRF4/MYC axis and exerts cooperative antimyeloma activity with bortezomib. Chem Biol Interact 2023; 384:110687. [PMID: 37657595 DOI: 10.1016/j.cbi.2023.110687] [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: 04/19/2023] [Revised: 08/13/2023] [Accepted: 08/26/2023] [Indexed: 09/03/2023]
Abstract
The activating protein-1 (AP-1) transcription factors (TFs) have been associated with many different cancer types and are promising therapeutic targets in logical malignancies. However, the mechanisms of their role in multiple myeloma (MM) remain elusive. The present study determined and compared the mRNA and protein expression levels of the AP-1 family member JunB in CD138+ mononuclear cells from MM patients and healthy donors. Herein, we investigated the effect of T-5224, an inhibitor of JUN/AP-1, on MM. We found that the cytotoxicity of T-5224 toward myeloma is due to its ability to induce cell apoptosis, inhibit proliferation, and induce cell cycle arrest by increasing the levels of cleaved caspase3/7 and concomitantly inhibiting the IRF4/MYC axis. We also noticed that siJunB-mediated deletion of JunB/AP-1 enhanced MM cell apoptosis and affected cell proliferation. The software PROMO was used in the present study to predict the AP-1 TF that may bind the promoter region of IRF4. We confirmed the correlation between JunB/AP-1 and IRF4. Given that bortezomib (BTZ) facilitates IRF4 degradation in MM cells, we applied combination treatment of BTZ with T-5224. T-5224 and BTZ exerted synergistic effects, and T-5224 reversed the effect of BTZ on CD138+ primary resistance in MM cells, in part due to suppression of the IRF4/MYC axis. Our results suggest that targeting AP-1 TFs is a promising therapeutic strategy for MM. Additionally, targeting both AP-1 and IRF4 with T-5224 may be a synergistic therapeutic strategy for this clinically challenging subset of MM.
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Affiliation(s)
- Sishi Tang
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Fangrong Zhang
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Jian Li
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, 410013, China
| | - Hang Dong
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, 410013, China
| | - Qin Yang
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Jing Liu
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, 410013, China.
| | - Yunfeng Fu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, 410013, China.
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9
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Ren FJ, Cai XY, Yao Y, Fang GY. JunB: a paradigm for Jun family in immune response and cancer. Front Cell Infect Microbiol 2023; 13:1222265. [PMID: 37731821 PMCID: PMC10507257 DOI: 10.3389/fcimb.2023.1222265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023] Open
Abstract
Jun B proto-oncogene (JunB) is a crucial member of dimeric activator protein-1 (AP-1) complex, which plays a significant role in various physiological processes, such as placental formation, cardiovascular development, myelopoiesis, angiogenesis, endochondral ossification and epidermis tissue homeostasis. Additionally, it has been reported that JunB has great regulatory functions in innate and adaptive immune responses by regulating the differentiation and cytokine secretion of immune cells including T cells, dendritic cells and macrophages, while also facilitating the effector of neutrophils and natural killer cells. Furthermore, a growing body of studies have shown that JunB is involved in tumorigenesis through regulating cell proliferation, differentiation, senescence and metastasis, particularly affecting the tumor microenvironment through transcriptional promotion or suppression of oncogenes in tumor cells or immune cells. This review summarizes the physiological function of JunB, its immune regulatory function, and its contribution to tumorigenesis, especially focusing on its regulatory mechanisms within tumor-associated immune processes.
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Affiliation(s)
- Fu-jia Ren
- Department of Pharmacy, Hangzhou Women’s Hospital, Hangzhou, Zhejiang, China
| | - Xiao-yu Cai
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yao Yao
- Department of Pharmacy, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guo-ying Fang
- Department of Pharmacy, Hangzhou Women’s Hospital, Hangzhou, Zhejiang, China
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10
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Duan M, Nguyen DC, Joyner CJ, Saney CL, Tipton CM, Andrews J, Lonial S, Kim C, Hentenaar I, Kosters A, Ghosn E, Jackson A, Knechtle S, Maruthamuthu S, Chandran S, Martin T, Rajalingam R, Vincenti F, Breeden C, Sanz I, Gibson G, Lee FEH. Understanding heterogeneity of human bone marrow plasma cell maturation and survival pathways by single-cell analyses. Cell Rep 2023; 42:112682. [PMID: 37355988 PMCID: PMC10391632 DOI: 10.1016/j.celrep.2023.112682] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/28/2022] [Accepted: 06/06/2023] [Indexed: 06/27/2023] Open
Abstract
Human bone marrow (BM) plasma cells are heterogeneous, ranging from newly arrived antibody-secreting cells (ASCs) to long-lived plasma cells (LLPCs). We provide single-cell transcriptional resolution of 17,347 BM ASCs from five healthy adults. Fifteen clusters are identified ranging from newly minted ASCs (cluster 1) expressing MKI67 and high major histocompatibility complex (MHC) class II that progress to late clusters 5-8 through intermediate clusters 2-4. Additional ASC clusters include the following: immunoglobulin (Ig) M predominant (likely of extra-follicular origin), interferon responsive, and high mitochondrial activity. Late ASCs are distinguished by G2M checkpoints, mammalian target of rapamycin (mTOR) signaling, distinct metabolic pathways, CD38 expression, utilization of tumor necrosis factor (TNF)-receptor superfamily members, and two distinct maturation pathways involving TNF signaling through nuclear factor κB (NF-κB). This study provides a single-cell atlas and molecular roadmap of LLPC maturation trajectories essential in the BM microniche. Altogether, understanding BM ASC heterogeneity in health and disease enables development of new strategies to enhance protective ASCs and to deplete pathogenic ones.
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Affiliation(s)
- Meixue Duan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Doan C Nguyen
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Chester J Joyner
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Celia L Saney
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Christopher M Tipton
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA; Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - Joel Andrews
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Caroline Kim
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Ian Hentenaar
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Astrid Kosters
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - Eliver Ghosn
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - Annette Jackson
- Departments of Immunology, Duke University, Durham, NC, USA; Department of Surgery, Duke University, Durham, NC, USA
| | | | - Stalinraja Maruthamuthu
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Sindhu Chandran
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Tom Martin
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Flavio Vincenti
- Division of Nephrology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cynthia Breeden
- Emory Transplant Center, Department of Surgery, School of Medicine, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA; Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA.
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11
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Liu Q, Yang T, Zhang Y, Hu ZD, Liu YM, Luo YL, Liu SX, Zhang H, Zhong Q. ZIC2 induces pro-tumor macrophage polarization in nasopharyngeal carcinoma by activating the JUNB/MCSF axis. Cell Death Dis 2023; 14:455. [PMID: 37479694 PMCID: PMC10362010 DOI: 10.1038/s41419-023-05983-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/19/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is a common malignant epithelial tumor of the head and neck that often exhibits local recurrence and distant metastasis. The molecular mechanisms are understudied, and effective therapeutic targets are still lacking. In our study, we found that the transcription factor ZIC2 was highly expressed in NPC. Although ZIC family members play important roles in neural development and carcinogenesis, the specific mechanism and clinical significance of ZIC2 in the tumorigenesis and immune regulation of NPC remain elusive. Here, we first reported that high expression of ZIC2 triggered the secretion of MCSF in NPC cells, induced M2 polarization of tumor-associated macrophages (TAMs), and affected the secretion of TAM-related cytokines. Mechanistically, ChIP-seq and RNA-seq analyses identified JUNB as a downstream target of ZIC2. Furthermore, ZIC2 was significantly enriched in the promoter site of JUNB and activated JUNB promoter activity, as shown by ChIP-qPCR and luciferase assays. In addition, JUNB and MCSF participated in ZIC2-induced M2 TAMs polarization. Thus, blocking JUNB and MCSF could reverse ZIC2-mediated M2 TAMs polarization. Moreover, Kaplan-Meier survival analyses indicated that high expression of ZIC2, JUNB, and CD163 was positively associated with a poor prognosis in NPC. Overexpression of ZIC2 induced tumor growth in vivo, with the increase of JUNB, MCSF secretion, and CD163. In summary, our study implies that ZIC2 induces M2 TAM polarization, at least in part through regulation of JUNB/MCSF and that ZIC2, JUNB, and CD163 can be utilized as prognostic markers for NPC and as therapeutic targets for cancer immunotherapy.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Department of Ultrasound Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ting Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Yu Zhang
- Department of Pathology, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Ze-Dong Hu
- Department of Orthopedics, The First People's Hospital of Anning, Kunming, China
| | - Yan-Min Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine; Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Yi-Ling Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Shang-Xin Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Hua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center (SYSUCC), Guangzhou, China.
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12
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Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023; 6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of therapy resistance. Since the cell of origin can impact response to therapy, it is crucial to understand the lineage composition of AML cells at time of therapy resistance. Here we leverage single-cell chromatin accessibility profiling of 22 AML bone marrow aspirates from eight patients at time of therapy resistance and following subsequent therapy to characterize their lineage landscape. Our findings reveal a complex lineage architecture of therapy-resistant AML cells that are primed for stem and progenitor lineages and spanning quiescent, activated and late stem cell/progenitor states. Remarkably, therapy-resistant AML cells are also composed of cells primed for differentiated myeloid, erythroid and even lymphoid lineages. The heterogeneous lineage composition persists following subsequent therapy, with early progenitor-driven features marking unfavorable prognosis in The Cancer Genome Atlas AML cohort. Pseudotime analysis further confirms the vast degree of heterogeneity driven by the dynamic changes in chromatin accessibility. Our findings suggest that therapy-resistant AML cells are characterized not only by stem and progenitor states, but also by a continuum of differentiated cellular lineages. The heterogeneity in lineages likely contributes to their therapy resistance by harboring different degrees of lineage-specific susceptibilities to therapy.
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Affiliation(s)
- Huihui Fan
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alex Murison
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katarzyna Tomczak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fatima Zahra Jelloul
- Department of Hematopathology, University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Bofei Wang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Praveen Barrodia
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kunal Rai
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Dick
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andy Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Abbas
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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13
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Duan M, Nguyen DC, Joyner CJ, Saney CL, Tipton CM, Andrews J, Lonial S, Kim C, Hentenaar I, Kosters A, Ghosn E, Jackson A, Knechtle S, Maruthamuthu S, Chandran S, Martin T, Rajalingam R, Vincenti F, Breeden C, Sanz I, Gibson G, Eun-Hyung Lee F. Human Bone Marrow Plasma Cell Atlas: Maturation and Survival Pathways Unraveled by Single Cell Analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524601. [PMID: 36711623 PMCID: PMC9882341 DOI: 10.1101/2023.01.18.524601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Human bone marrow (BM) plasma cells are heterogeneous, ranging from newly arrived antibody-secreting cells (ASC) to long-lived plasma cells (LLPC). We provide single cell transcriptional resolution of 17,347 BM ASC from 5 healthy adults. Fifteen clusters were identified ranging from newly minted ASC (cluster 1) expressing MKI67 and high MHC Class II that progressed to late clusters 5-8 through intermediate clusters 2-4. Additional clusters included early and late IgM-predominant ASC of likely extra-follicular origin; IFN-responsive; and high mitochondrial activity ASC. Late ASCs were distinguished by differences in G2M checkpoints, MTOR signaling, distinct metabolic pathways, CD38 expression, and utilization of TNF-receptor superfamily members. They mature through two distinct paths differentiated by the degree of TNF signaling through NFKB. This study provides the first single cell resolution atlas and molecular roadmap of LLPC maturation, thereby providing insight into differentiation trajectories and molecular regulation of these essential processes in the human BM microniche. This information enables investigation of the origin of protective and pathogenic antibodies in multiple diseases and development of new strategies targeted to the enhancement or depletion of the corresponding ASC. One Sentence Summary: The single cell transcriptomic atlas of human bone marrow plasma cell heterogeneity shows maturation of class-switched early and late subsets, specific IgM and Interferon-driven clusters, and unique heterogeneity of the late subsets which encompass the long-lived plasma cells.
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14
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Evaluation of Genes and Molecular Pathways Involved in the Progression of Monoclonal Gammopathy of Undetermined Significance (MGUS) to Multiple Myeloma: A Systems Biology Approach. Mol Biotechnol 2022:10.1007/s12033-022-00634-6. [DOI: 10.1007/s12033-022-00634-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022]
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15
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Jung SH, Park SS, Lim JY, Sohn SY, Kim NY, Kim D, Lee SH, Chung YJ, Min CK. Single-cell analysis of multiple myelomas refines the molecular features of bortezomib treatment responsiveness. Exp Mol Med 2022; 54:1967-1978. [PMID: 36380017 PMCID: PMC9723182 DOI: 10.1038/s12276-022-00884-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/25/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Both the tumor and tumor microenvironment (TME) are crucial for pathogenesis and chemotherapy resistance in multiple myeloma (MM). Bortezomib, commonly used for MM treatment, works on both MM and TME cells, but innate and acquired resistance easily develop. By single-cell RNA sequencing (scRNA-seq), we investigated bone marrow aspirates of 18 treatment-naïve MM patients who later received bortezomib-based treatments. Twelve plasma and TME cell types and their subsets were identified. Suboptimal responders (SORs) to bortezomib exhibited higher copy number alteration burdens than optimal responders (ORs). Forty-four differentially expressed genes for SORs based on scRNA-seq data were further analyzed in an independent cohort of 90 treatment-naïve MMs, where 24 genes were validated. A combined model of three clinical variables (older age, low absolute lymphocyte count, and no autologous stem cell transplantation) and 24 genes was associated with bortezomib responsiveness and poor prognosis. In T cells, cytotoxic memory, proliferating, and dysfunctional subsets were significantly enriched in SORs. Moreover, we identified three monocyte subsets associated with bortezomib responsiveness and an MM-specific NK cell trajectory that ended with an MM-specific subset. scRNA-seq predicted the interaction of the GAS6-MERTK, ALCAM-CD6, and BAG6-NCR gene networks. Of note, tumor cells from ORs and SORs were the most prominent sources of ALCAM on effector T cells and BAG6 on NK cells, respectively. Our results indicate that the complicated compositional and molecular changes of both tumor and immune cells in the bone marrow (BM) milieu are important in the development and acquisition of resistance to bortezomib-based treatment of MM.
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Affiliation(s)
- Seung-Hyun Jung
- grid.411947.e0000 0004 0470 4224Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sung-Soo Park
- Department of Hematology, Seoul St. Mary’s Hematology Hospital, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Ji-Young Lim
- Department of Hematology, Seoul St. Mary’s Hematology Hospital, Seoul, South Korea
| | - Seon Yong Sohn
- grid.411947.e0000 0004 0470 4224Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Na Yung Kim
- grid.411947.e0000 0004 0470 4224Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Dokyeong Kim
- grid.411947.e0000 0004 0470 4224Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Precision Medicine Research Center/IRCGP, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sug Hyung Lee
- grid.411947.e0000 0004 0470 4224Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Yeun-Jun Chung
- grid.411947.e0000 0004 0470 4224Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Precision Medicine Research Center/IRCGP, College of Medicine, The Catholic University of Korea, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Chang-Ki Min
- Department of Hematology, Seoul St. Mary’s Hematology Hospital, Seoul, South Korea ,grid.411947.e0000 0004 0470 4224Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, South Korea
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16
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Børset M, Elsaadi S, Vandsemb EN, Hess ES, Steiro IJ, Cocera Fernandez M, Sponaas AM, Abdollahi P. Highly expressed genes in multiple myeloma cells - what can they tell us about the disease? Eur J Haematol Suppl 2022; 109:31-40. [PMID: 35276027 PMCID: PMC9310595 DOI: 10.1111/ejh.13766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/29/2022]
Abstract
Cancer cells can convert proto‐oncoproteins into oncoproteins by increasing the expression of genes that are oncogenic when expressed at high levels. Such genes can promote oncogenesis without being mutated. To find overexpressed genes in cancer cells from patients with multiple myeloma, we retrieved mRNA expression data from the CoMMpass database and ranked genes by their expression levels. We grouped the most highly expressed genes based on a set of criteria and we discuss the role a selection of them can play in the disease pathophysiology. The list was highly concordant with a similar list based on mRNA expression data from the PADIMAC study. Many well‐known “myeloma genes” such as MCL1, CXCR4, TNFRSF17, SDC1, SLAMF7, PTP4A3, and XBP1 were identified as highly expressed, and we believe that hitherto unrecognized key players in myeloma pathogenesis are also enriched on the list. Highly expressed genes in malignant plasma cells that were absent or expressed at only a low level in healthy plasma cells included IFI6, IFITM1, PTP4A3, SIK1, ALDOA, ATP5MF, ATP5ME, and PSMB4. The ambition of this article is not to validate the role of each gene but to serve as a guide for studies aiming at identifying promising treatment targets.
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Affiliation(s)
- Magne Børset
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Immunology and Transfusion Medicine, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Samah Elsaadi
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Esten N Vandsemb
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Eli Svorkdal Hess
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ida J Steiro
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miguel Cocera Fernandez
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anne-Marit Sponaas
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Pegah Abdollahi
- Department of Clinical and Molecular Medicine, Center for Myeloma Research, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Laboratory Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
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17
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Masuda T, Haji S, Nakashima Y, Tsuda M, Kimura D, Takamatsu A, Iwahashi N, Umakoshi H, Shiratsuchi M, Kikutake C, Suyama M, Ohkawa Y, Ogawa Y. Identification of a drug-response gene in multiple myeloma through longitudinal single-cell transcriptome sequencing. iScience 2022; 25:104781. [PMID: 35992084 PMCID: PMC9386061 DOI: 10.1016/j.isci.2022.104781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/06/2022] Open
Abstract
Despite recent therapeutic advances for multiple myeloma (MM), relapse is very common. Here, we conducted longitudinal single-cell transcriptome sequencing (scRNA-seq) of MM cells from a patient with relapsed MM, treated with multiple anti-myeloma drugs. We observed five subclusters of MM cells, which appeared and/or disappeared in response to the therapeutic pressure, and identified cluster 3 which emerged during lenalidomide treatment and disappeared after proteasome inhibitor (PI) treatment. Among the differentially expressed genes in cluster 3, we found a candidate drug-response gene; pellino E3 ubiquitin-protein ligase family member 2 (PELI2), which is responsible for PI-induced cell death in in vitro assay. Kaplan-Meier survival analysis of database revealed that higher expression of PELI2 is associated with a better prognosis. Our integrated strategy combining longitudinal scRNA-seq analysis, in vitro functional assay, and database analysis would facilitate the understanding of clonal dynamics of MM in response to anti-myeloma drugs and identification of drug-response genes. Longitudinal scRNA-seq reveals clonal dynamics of MM under therapeutic pressure PELI2 is identified as a candidate proteasome inhibitors (PI)-sensitive gene from the PI-sensitive cluster Overexpression of PELI2 sensitizes PI to an MM cell line in the cytotoxic assay In database analysis, high expression of PELI2 is associated with a better prognosis
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18
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Cheng L, Li Y, Yao Y, Jin X, Ying H, Xu B, Xu J. Toxic Effects of Thioacetamide-Induced Femoral Damage in New Zealand White Rabbits by Activating the p38/ERK Signaling Pathway. Physiol Res 2022; 71:285-295. [DOI: 10.33549/physiolres.934803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Thioacetamide (TAA) is widely used in the production of drugs, pesticides and dyeing auxiliaries. Moreover, it is a chemical that can cause liver damage and cancer. TAA has recently been identified to cause bone damage in animal models. However, the type of bone damage that TAA causes and its potential pathogenic mechanisms remain unclear. The toxic effects of TAA on the femurs of New Zealand white rabbits and the underlying toxicity mechanism were investigated in this study. Serum samples, the heart, liver, kidney and femurs were collected from rabbits after intraperitoneal injection of TAA for 5 months (100 and 200 mg/kg). The New Zealand white rabbits treated with TAA showed significant weight loss and femoral shortening. The activities of total bilirubin, total bile acid and gamma-glutamyl transpeptidase in the serum were increased following treatment with TAA. In addition, the cortical bone became thinner, and the trabecular thickness decreased significantly in TAA-treated rabbits, which was accompanied by significantly decreased mineral density of the cortical and trabecular bone. Moreover, there was a significant decrease in modulus of elasticity and maximum load on bone stress in TAA-treated rabbits. The western blotting results showed that the expression of phosphorylated (p)-p38 and p-ERK in femur tissues of rabbits were increased after TAA administration. Collectively, these results suggested that TAA may lead to femoral damage in rabbits by activating the p38/ERK signaling pathway.
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Affiliation(s)
| | | | | | | | | | | | - J Xu
- School of Medical Technology and Information Engineering, Zhejiang, Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China, e-mail:
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19
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Zhang B, Lin J, Zhang J, Wang X, Deng X. Integrated Chromatin Accessibility and Transcriptome Landscapes of 5-Fluorouracil-Resistant Colon Cancer Cells. Front Cell Dev Biol 2022; 10:838332. [PMID: 35252200 PMCID: PMC8891516 DOI: 10.3389/fcell.2022.838332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 12/11/2022] Open
Abstract
Background: 5-Fluorouracil (5-FU) is one of the most effective and widely used chemotherapeutic drugs in the treatment of colon cancer, yet chemoresistance is a common feature of colon cancer treatment, resulting in poor prognosis and short survival. Dynamic reprogramming of chromatin accessibility is crucial for proper regulation of gene transcription associated with cancer drug resistance by providing the gene regulatory machinery with rapid access to the open genomic DNA. Methods: Here, we explored the global chromatin accessibility and transcription changes by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with transcriptome sequencing of both parental and 5-FU-resistant HCT15 cells, followed by integrative analysis to better understand the regulatory network underlying 5-FU resistance in colon cancer cells. Results: A total of 3,175 differentially expressed mRNAs (DEGs), lncRNAs (DELs), and miRNAs (DEMs) related to 5-FU resistance were identified, including significantly upregulated IL33, H19, and miR-17-5p; the downregulated AKR1B10, LINC01012, and miR-125b-5p; and chromatin modifiers such as INO80C, HDAC6, and KDM5A. The construction of the ceRNA regulatory network revealed that H19, HOXA11-AS, and NEAT1 might function as ceRNAs associated with 5-FU resistance in HCT15 cells. Moreover, 9,868 differentially accessible regions (DARs) were obtained, which were positively (r = 0.58) correlated with their nearest DEGs and DELs. The upregulated genes related to 4,937 hyper-accessible regions were significantly enriched in signaling pathways of MAPK, FOX, and WNT, while the 4,931 hypo-accessible regions were considered to be involved in declined biosynthesis of amino acids and nucleotide sugars, signaling pathways of Notch, and HIF-1. Analyses of the DAR sequences revealed that besides the AP-1 family, the TF motifs of FOX and KLF family members were highly enriched in hyper- and hypo-accessible regions, respectively. Finally, we obtained several critical TFs and their potential targets associated with DARs and 5-FU resistance, including FOXA1 and KLF3. Conclusion: These data provided clear insights and valuable resources for an improved understanding of the non-genetic landscape of 5-FU-resistant colon cancer cells based on chromatin accessibility and transcript levels, which allowed for genome-wide detection of TF binding sites, potential cis-regulatory elements and therapeutic targets.
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Affiliation(s)
- Bishu Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiewei Lin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqiang Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Jiaqiang Zhang, ; Xuelong Wang, ; Xiaxing Deng,
| | - Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Jiaqiang Zhang, ; Xuelong Wang, ; Xiaxing Deng,
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Jiaqiang Zhang, ; Xuelong Wang, ; Xiaxing Deng,
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Dziadowicz SA, Wang L, Akhter H, Aesoph D, Sharma T, Adjeroh DA, Hazlehurst LA, Hu G. Bone Marrow Stroma-Induced Transcriptome and Regulome Signatures of Multiple Myeloma. Cancers (Basel) 2022; 14:927. [PMID: 35205675 PMCID: PMC8870223 DOI: 10.3390/cancers14040927] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
Multiple myeloma (MM) is a hematological cancer with inevitable drug resistance. MM cells interacting with bone marrow stromal cells (BMSCs) undergo substantial changes in the transcriptome and develop de novo multi-drug resistance. As a critical component in transcriptional regulation, how the chromatin landscape is transformed in MM cells exposed to BMSCs and contributes to the transcriptional response to BMSCs remains elusive. We profiled the transcriptome and regulome for MM cells using a transwell coculture system with BMSCs. The transcriptome and regulome of MM cells from the upper transwell resembled MM cells that coexisted with BMSCs from the lower chamber but were distinctive to monoculture. BMSC-induced genes were enriched in the JAK2/STAT3 signaling pathway, unfolded protein stress, signatures of early plasma cells, and response to proteasome inhibitors. Genes with increasing accessibility at multiple regulatory sites were preferentially induced by BMSCs; these genes were enriched in functions linked to responses to drugs and unfavorable clinic outcomes. We proposed JUNB and ATF4::CEBPβ as candidate transcription factors (TFs) that modulate the BMSC-induced transformation of the regulome linked to the transcriptional response. Together, we characterized the BMSC-induced transcriptome and regulome signatures of MM cells to facilitate research on epigenetic mechanisms of BMSC-induced multi-drug resistance in MM.
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Affiliation(s)
- Sebastian A. Dziadowicz
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
| | - Lei Wang
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
| | - Halima Akhter
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
- Lane Department of Computer Science & Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA;
| | - Drake Aesoph
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
- Lane Department of Computer Science & Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA;
| | - Tulika Sharma
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
| | - Donald A. Adjeroh
- Lane Department of Computer Science & Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA;
| | - Lori A. Hazlehurst
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA;
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morganton, WV 26506, USA
| | - Gangqing Hu
- Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26505, USA; (S.A.D.); (L.W.); (H.A.); (D.A.); (T.S.)
- WVU Cancer Institute, West Virginia University, Morgantown, WV 26506, USA;
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21
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Schütt J, Nägler T, Schenk T, Brioli A. Investigating the Interplay between Myeloma Cells and Bone Marrow Stromal Cells in the Development of Drug Resistance: Dissecting the Role of Epigenetic Modifications. Cancers (Basel) 2021; 13:cancers13164069. [PMID: 34439223 PMCID: PMC8392438 DOI: 10.3390/cancers13164069] [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: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Despite advances made in the last two decades, multiple myeloma (MM) is still an incurable disease. The genetic complexity of MM and the presence of intra-clonal heterogeneity are major contributors to disease relapse and the development of treatment resistance. Additionally, the bone marrow microenvironment is known to play a pivotal role in MM disease progression. Together with genetic modifications, epigenetic changes have been shown to influence MM development and progression. However, epigenetic treatments for MM are still lacking. This is mainly due to the high rate of adverse events of epigenetic drugs in clinical practice. In this review, we will focus on the role of epigenetic modifications in MM disease progression and the development of drug resistance, as well as their role in shaping the interplay between bone marrow stromal cells and MM cells. The current and future treatment strategies involving epigenetic drugs will also be addressed. Abstract Multiple Myeloma (MM) is a malignancy of plasma cells infiltrating the bone marrow (BM). Many studies have demonstrated the crucial involvement of bone marrow stromal cells in MM progression and drug resistance. Together with the BM microenvironment (BMME), epigenetics also plays a crucial role in MM development. A variety of epigenetic regulators, including histone acetyltransferases (HATs), histone methyltransferases (HMTs) and lysine demethylases (KDMs), are altered in MM, contributing to the disease progression and prognosis. In addition to histone modifications, DNA methylation also plays a crucial role. Among others, aberrant epigenetics involves processes associated with the BMME, like bone homeostasis, ECM remodeling or the development of treatment resistance. In this review, we will highlight the importance of the interplay of MM cells with the BMME in the development of treatment resistance. Additionally, we will focus on the epigenetic aberrations in MM and their role in disease evolution, interaction with the BMME, disease progression and development of drug resistance. We will also briefly touch on the epigenetic treatments currently available or currently under investigation to overcome BMME-driven treatment resistance.
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Affiliation(s)
- Jacqueline Schütt
- Clinic of Internal Medicine 2, Hematology and Oncology, Jena University Hospital, 07747 Jena, Germany
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB), Jena University Hospital, 07747 Jena, Germany
- Clinic of Internal Medicine C, Hematology and Oncology, Stem Cell Transplantation and Palliative Care, Greifswald University Medicine, 17475 Greifswald, Germany
| | - Theresa Nägler
- Clinic of Internal Medicine 2, Hematology and Oncology, Jena University Hospital, 07747 Jena, Germany
| | - Tino Schenk
- Clinic of Internal Medicine 2, Hematology and Oncology, Jena University Hospital, 07747 Jena, Germany
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB), Jena University Hospital, 07747 Jena, Germany
- Clinic of Internal Medicine C, Hematology and Oncology, Stem Cell Transplantation and Palliative Care, Greifswald University Medicine, 17475 Greifswald, Germany
| | - Annamaria Brioli
- Clinic of Internal Medicine 2, Hematology and Oncology, Jena University Hospital, 07747 Jena, Germany
- Clinic of Internal Medicine C, Hematology and Oncology, Stem Cell Transplantation and Palliative Care, Greifswald University Medicine, 17475 Greifswald, Germany
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22
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Wang X, Yan J, Shen B, Wei G. Integrated Chromatin Accessibility and Transcriptome Landscapes of Doxorubicin-Resistant Breast Cancer Cells. Front Cell Dev Biol 2021; 9:708066. [PMID: 34395436 PMCID: PMC8363264 DOI: 10.3389/fcell.2021.708066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/12/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Doxorubicin is one of the most effective chemotherapeutic drugs for breast cancer while its common drug resistance leads to poor patient prognosis and survival. Growing evidence indicate dynamically reorganized chromatin allows rapid access of the gene regulatory machinery to open genomic regions facilitating subsequent gene expression through direct transcription factor (TF) activation and regulatory element binding. METHODS To better understand the regulatory network underlying doxorubicin resistance in breast cancer cells, we explored the systematic alterations of chromatin accessibility and gene expression by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with RNA sequencing, followed by integrative analysis to identify potential regulators and their targets associated with differentially accessible regions (DARs) in doxorubicin-resistant MCF7 (MCF7-DR) cells. RESULTS A total of 3,963 differentially expressed genes (DEGs) related to doxorubicin resistance were identified, including dramatically up-regulated MT1E, GSTP1, LDHB, significantly down-regulated TFF1, UBB, DSCAM-AS1, and histone-modifying enzyme coding genes HDAC2, EZH2, PRMT5, etc. By integrating with transcriptomic datasets, we identified 18,228 DARs in MCF7-DR cells compared to control, which were positively correlated with their nearest DEGs (r = 0.6). There were 11,686 increased chromatin-accessible regions, which were enriched in up-regulated genes related to diverse KEGG pathways, such as the cell cycle, regulation of actin cytoskeleton, signaling pathways of MAPK, PI3K/Akt and Hippo, which play essential roles in regulating cell apoptosis, proliferation, metabolism, and inflammatory responses. The 6,542 decreased chromatin-accessible regions were identified for the declined doxorubicin-associated biological processes, for instance, endocrine and insulin resistance, central carbon metabolism, signaling pathways of TGF-beta and P53. Combining data from TCGA, analyses of the DAR sequences associated with the DNA-binding motifs of significantly enriched TF families including AP-1, TEAD and FOX, indicated that the loss-function of FOXA1 might play a critical role in doxorubicin-resistant breast cancer cells (DOX-R BCCs). CONCLUSION These data exhibit the non-genetic landscape of chromatin accessibility and transcript levels in the DOX-R BCCs, and provide clear insights and resources for the detection of critical TFs and potential cis-regulatory elements-based putative therapeutic targets.
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Affiliation(s)
- Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jizhou Yan
- Department of Developmental Biology, Institute for Marine Biosystem and Neurosciences, Shanghai Ocean University, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai JiaoTong University School of Medicine, Shanghai, China
- Institute of Translational Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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Srivastava M, Kaplan MH. Transcription Factors in the Development and Pro-Allergic Function of Mast Cells. FRONTIERS IN ALLERGY 2021; 2:679121. [PMID: 35387064 PMCID: PMC8974754 DOI: 10.3389/falgy.2021.679121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Mast cells (MCs) are innate immune cells of hematopoietic origin localized in the mucosal tissues of the body and are broadly implicated in the pathogenesis of allergic inflammation. Transcription factors have a pivotal role in the development and differentiation of mast cells in response to various microenvironmental signals encountered in the resident tissues. Understanding the regulation of mast cells by transcription factors is therefore vital for mechanistic insights into allergic diseases. In this review we summarize advances in defining the transcription factors that impact the development of mast cells throughout the body and in specific tissues, and factors that are involved in responding to the extracellular milieu. We will further describe the complex networks of transcription factors that impact mast cell physiology and expansion during allergic inflammation and functions from degranulation to cytokine secretion. As our understanding of the heterogeneity of mast cells becomes more detailed, the contribution of specific transcription factors in mast cell-dependent functions will potentially offer new pathways for therapeutic targeting.
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Affiliation(s)
- Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University, Indianapolis, IN, United States
| | - Mark H. Kaplan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Mark H. Kaplan
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Targeting Reactive Oxygen Species Metabolism to Induce Myeloma Cell Death. Cancers (Basel) 2021; 13:cancers13102411. [PMID: 34067602 PMCID: PMC8156203 DOI: 10.3390/cancers13102411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a common hematological disease characterized by the accumulation of clonal malignant plasma cells in the bone marrow. Over the past two decades, new therapeutic strategies have significantly improved the treatment outcome and patients survival. Nevertheless, most MM patients relapse underlying the need of new therapeutic approaches. Plasma cells are prone to produce large amounts of immunoglobulins causing the production of intracellular ROS. Although adapted to high level of ROS, MM cells die when exposed to drugs increasing ROS production either directly or by inhibiting antioxidant enzymes. In this review, we discuss the efficacy of ROS-generating drugs for inducing MM cell death and counteracting acquired drug resistance specifically toward proteasome inhibitors.
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25
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Lombardo JA, Aliaghaei M, Nguyen QH, Kessenbrock K, Haun JB. Microfluidic platform accelerates tissue processing into single cells for molecular analysis and primary culture models. Nat Commun 2021; 12:2858. [PMID: 34001902 PMCID: PMC8128882 DOI: 10.1038/s41467-021-23238-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 04/20/2021] [Indexed: 02/03/2023] Open
Abstract
Tissues are complex mixtures of different cell subtypes, and this diversity is increasingly characterized using high-throughput single cell analysis methods. However, these efforts are hindered, as tissues must first be dissociated into single cell suspensions using methods that are often inefficient, labor-intensive, highly variable, and potentially biased towards certain cell subtypes. Here, we present a microfluidic platform consisting of three tissue processing technologies that combine tissue digestion, disaggregation, and filtration. The platform is evaluated using a diverse array of tissues. For kidney and mammary tumor, microfluidic processing produces 2.5-fold more single cells. Single cell RNA sequencing further reveals that endothelial cells, fibroblasts, and basal epithelium are enriched without affecting stress response. For liver and heart, processing time is dramatically reduced. We also demonstrate that recovery of cells from the system at periodic intervals during processing increases hepatocyte and cardiomyocyte numbers, as well as increases reproducibility from batch-to-batch for all tissues.
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Affiliation(s)
- Jeremy A Lombardo
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Marzieh Aliaghaei
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Quy H Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Jered B Haun
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA.
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA, USA.
- Center for Advanced Design and Manufacturing of Integrated Microfluidics, University of California, Irvine, Irvine, CA, USA.
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Fan F, Podar K. The Role of AP-1 Transcription Factors in Plasma Cell Biology and Multiple Myeloma Pathophysiology. Cancers (Basel) 2021; 13:2326. [PMID: 34066181 PMCID: PMC8151277 DOI: 10.3390/cancers13102326] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Multiple myeloma (MM) is an incurable hematologic malignancy characterized by the clonal expansion of malignant plasma cells within the bone marrow. Activator Protein-1 (AP-1) transcription factors (TFs), comprised of the JUN, FOS, ATF and MAF multigene families, are implicated in a plethora of physiologic processes and tumorigenesis including plasma cell differentiation and MM pathogenesis. Depending on the genetic background, the tumor stage, and cues of the tumor microenvironment, specific dimeric AP-1 complexes are formed. For example, AP-1 complexes containing Fra-1, Fra-2 and B-ATF play central roles in the transcriptional control of B cell development and plasma cell differentiation, while dysregulation of AP-1 family members c-Maf, c-Jun, and JunB is associated with MM cell proliferation, survival, drug resistance, bone marrow angiogenesis, and bone disease. The present review article summarizes our up-to-date knowledge on the role of AP-1 family members in plasma cell differentiation and MM pathophysiology. Moreover, it discusses novel, rationally derived approaches to therapeutically target AP-1 TFs, including protein-protein and protein-DNA binding inhibitors, epigenetic modifiers and natural products.
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Affiliation(s)
- Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1277, Wuhan 430022, China;
| | - Klaus Podar
- Department of Internal Medicine II, University Hospital Krems, Mitterweg 10, 3500 Krems an der Donau, Austria
- Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems an der Donau, Austria
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Łuczkowska K, Sokolowska KE, Taryma-Lesniak O, Pastuszak K, Supernat A, Bybjerg-Grauholm J, Hansen LL, Paczkowska E, Wojdacz TK, Machaliński B. Bortezomib induces methylation changes in neuroblastoma cells that appear to play a significant role in resistance development to this compound. Sci Rep 2021; 11:9846. [PMID: 33972578 PMCID: PMC8110815 DOI: 10.1038/s41598-021-89128-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
The anticancer activity of bortezomib (BTZ) has been increasingly studied in a number of indications and promising results for the use of this treatment have been shown in neuroblastoma. As BTZ treatment is usually administered in cycles, the development of resistance and side effects in patients undergoing therapy with BTZ remains a major challenge for the clinical usage of this compound. Common resistance development also means that certain cells are able to survive BTZ treatment and bypass molecular mechanisms that render BTZ anticancer activity. We studied the methylome of neuroblastoma cells that survived BTZ treatment. Our results indicate that BTZ induces pronounced genome wide methylation changes in cells which recovered from the treatment. Functional analyses of identified methylation changes demonstrated they were involved in key cancer pathology pathways. These changes may allow the cells to bypass the primary anticancer activity of BTZ and develop a treatment resistant and proliferative phenotype. To study whether cells surviving BTZ treatment acquire a proliferative phenotype, we repeatedly treated cells which recovered from the first round of BTZ treatment. The repetitive treatment led to induction of the extraordinary proliferative potential of the cells, that increased with subsequent treatments. As we did not observe similar effects in cells that survived treatment with lenalidomide, and non-treated cells cultured under the same experimental conditions, this phenomenon seems to be BTZ specific. Overall, our results indicate that methylation changes may play major role in the development of BTZ resistance.
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Affiliation(s)
- Karolina Łuczkowska
- Department of General Pathology, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111, Szczecin, Poland
| | - Katarzyna Ewa Sokolowska
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Olga Taryma-Lesniak
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Krzysztof Pastuszak
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland.,Department of Algorithms and Systems Modelling, Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Anna Supernat
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, 2300, København S Copenhagen, Denmark
| | - Lise Lotte Hansen
- Department of Biomedicine, Aarhus University, Hoegh-Guldbergsgade 10, 8000, Aarhus, Denmark
| | - Edyta Paczkowska
- Department of General Pathology, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111, Szczecin, Poland
| | - Tomasz K Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252, Szczecin, Poland. .,Department of Biomedicine, Aarhus University, Hoegh-Guldbergsgade 10, 8000, Aarhus, Denmark. .,Aarhus Institute of Advanced Studies, Hoegh-Guldbergs Gade 6B, 8000, Aarhus, Denmark.
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, Powstańców Wlkp. 72, 70-111, Szczecin, Poland.
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Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing. Cells 2021; 10:cells10050973. [PMID: 33919312 PMCID: PMC8143332 DOI: 10.3390/cells10050973] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
(1) Background: mouse models are fundamental to the study of hematopoiesis, but comparisons between mouse and human in single cells have been limited in depth. (2) Methods: we constructed a single-cell resolution transcriptomic atlas of hematopoietic stem and progenitor cells (HSPCs) of human and mouse, from a total of 32,805 single cells. We used Monocle to examine the trajectories of hematopoietic differentiation, and SCENIC to analyze gene networks underlying hematopoiesis. (3) Results: After alignment with Seurat 2, the cells of mouse and human could be separated by same cell type categories. Cells were grouped into 17 subpopulations; cluster-specific genes were species-conserved and shared functional themes. The clustering dendrogram indicated that cell types were highly conserved between human and mouse. A visualization of the Monocle results provided an intuitive representation of HSPC differentiation to three dominant branches (Erythroid/megakaryocytic, Myeloid, and Lymphoid), derived directly from the hematopoietic stem cell and the long-term hematopoietic stem cells in both human and mouse. Gene regulation was similarly conserved, reflected by comparable transcriptional factors and regulatory sequence motifs in subpopulations of cells. (4) Conclusions: our analysis has confirmed evolutionary conservation in the hematopoietic systems of mouse and human, extending to cell types, gene expression and regulatory elements.
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Zhao X, Xing J, Li J, Hou R, Niu X, Liu R, Jiao J, Yang X, Li J, Liang J, Zhou L, Wang Q, Chang W, Yin G, Li X, Zhang K. Dysregulated Dermal Mesenchymal Stem Cell Proliferation and Differentiation Interfered by Glucose Metabolism in Psoriasis. Int J Stem Cells 2021; 14:85-93. [PMID: 33632981 PMCID: PMC7904530 DOI: 10.15283/ijsc20073] [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: 05/01/2020] [Revised: 09/30/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
Background and Objectives Psoriasis is a chronic inflammatory skin disease, which the mechanisms behind its initiation and development are related to many factors. DMSCs (dermal mesenchymal stem cells) represent an important member of the skin microenvironment and play an important role in the surrounding environment and in neighbouring cells, but they are also affected by the microenvironment. We studied the glucose metabolism of DMSCs in psoriasis patients and a control group to reveal the relationship among glucose metabolism, cell proliferation activity,and VEC (vascular endothelial cell) differentiation in vitro, we demonstrated the biological activity and molecular mechanisms of DMSCs in psoriasis. Methods and Results We found that the OCR of DMSCs in psoriatic lesions was higher than that in the control group, and mRNA of GLUT1 and HK2 were up-regulated compared with the control group. The proliferative activity of DMSCs in psoriasis was reduced at an early stage, and mRNA involved in proliferation, JUNB and FOS were expressed at lower levels than those in the control group. The number of blood vessels in psoriatic lesions was significantly higher than that in the control group (p<0.05), which the mRNA of VEC differentiation, CXCL12, CXCR7, HEYL and RGS5 tended to be increased in psoriatic lesions compared to the control group, in addition to Notch3. Conclusions We speculated that DMSCs affected local psoriatic blood vessels through glucose metabolism, and the differentiation of VECs, which resulted in the pathophysiological process of psoriasis.
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Affiliation(s)
- Xincheng Zhao
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianxiao Xing
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Junqin Li
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Ruixia Hou
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Xuping Niu
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Ruifeng Liu
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Juanjuan Jiao
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiaohong Yang
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Juan Li
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Jiannan Liang
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Ling Zhou
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Qiang Wang
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Wenjuan Chang
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Guohua Yin
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Xinhua Li
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
| | - Kaiming Zhang
- Shanxi Key Laboratory of Stem Cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital of Shanxi Medical University, Taiyuan, China
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30
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Wu Z, Nicoll M, Ingham RJ. AP-1 family transcription factors: a diverse family of proteins that regulate varied cellular activities in classical hodgkin lymphoma and ALK+ ALCL. Exp Hematol Oncol 2021; 10:4. [PMID: 33413671 PMCID: PMC7792353 DOI: 10.1186/s40164-020-00197-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/07/2023] Open
Abstract
Classical Hodgkin lymphoma (cHL) and anaplastic lymphoma kinase-positive, anaplastic large cell lymphoma (ALK+ ALCL) are B and T cell lymphomas respectively, which express the tumour necrosis factor receptor superfamily member, CD30. Another feature shared by cHL and ALK+ ALCL is the aberrant expression of multiple members of the activator protein-1 (AP-1) family of transcription factors which includes proteins of the Jun, Fos, ATF, and Maf subfamilies. In this review, we highlight the varied roles these proteins play in the pathobiology of these lymphomas including promoting proliferation, suppressing apoptosis, and evading the host immune response. In addition, we discuss factors contributing to the elevated expression of these transcription factors in cHL and ALK+ ALCL. Finally, we examine therapeutic strategies for these lymphomas that exploit AP-1 transcriptional targets or the signalling pathways they regulate.
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Affiliation(s)
- Zuoqiao Wu
- grid.17089.37Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada ,grid.17063.330000 0001 2157 2938Present Address: Department of Medicine, University of Toronto, Toronto, Canada
| | - Mary Nicoll
- grid.17089.37Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada ,grid.14709.3b0000 0004 1936 8649Present Address: Department of Biology, McGill University, Montreal, Canada
| | - Robert J. Ingham
- grid.17089.37Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
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31
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Fan F, Malvestiti S, Vallet S, Lind J, Garcia-Manteiga JM, Morelli E, Jiang Q, Seckinger A, Hose D, Goldschmidt H, Stadlbauer A, Sun C, Mei H, Pecherstorfer M, Bakiri L, Wagner EF, Tonon G, Sattler M, Hu Y, Tassone P, Jaeger D, Podar K. JunB is a key regulator of multiple myeloma bone marrow angiogenesis. Leukemia 2021; 35:3509-3525. [PMID: 34007044 PMCID: PMC8632680 DOI: 10.1038/s41375-021-01271-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/14/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
Bone marrow (BM) angiogenesis significantly influences disease progression in multiple myeloma (MM) patients and correlates with adverse prognosis. The present study shows a statistically significant correlation of the AP-1 family member JunB with VEGF, VEGFB, and IGF1 expression levels in MM. In contrast to the angiogenic master regulator Hif-1α, JunB protein levels were independent of hypoxia. Results in tumor-cell models that allow the induction of JunB knockdown or JunB activation, respectively, corroborated the functional role of JunB in the production and secretion of these angiogenic factors (AFs). Consequently, conditioned media derived from MM cells after JunB knockdown or JunB activation either inhibited or stimulated in vitro angiogenesis. The impact of JunB on MM BM angiogenesis was finally confirmed in a dynamic 3D model of the BM microenvironment, a xenograft mouse model as well as in patient-derived BM sections. In summary, in continuation of our previous study (Fan et al., 2017), the present report reveals for the first time that JunB is not only a mediator of MM cell survival, proliferation, and drug resistance, but also a promoter of AF transcription and consequently of MM BM angiogenesis. Our results thereby underscore worldwide efforts to target AP-1 transcription factors such as JunB as a promising strategy in MM therapy.
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Affiliation(s)
- Fengjuan Fan
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China ,grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Stefano Malvestiti
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Sonia Vallet
- grid.488547.2Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria ,grid.459693.4Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Judith Lind
- grid.459693.4Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Jose Manuel Garcia-Manteiga
- grid.18887.3e0000000417581884Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eugenio Morelli
- grid.411489.10000 0001 2168 2547Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Qinyue Jiang
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Anja Seckinger
- grid.5253.10000 0001 0328 4908University Hospital Heidelberg, Heidelberg, Germany ,grid.8767.e0000 0001 2290 8069Laboratory of Hematology and Immunology & Laboratory for Myeloma Research, Vrije Universiteit Brussel (VUB) Belgium, Brussels, Belgium
| | - Dirk Hose
- grid.5253.10000 0001 0328 4908University Hospital Heidelberg, Heidelberg, Germany ,grid.8767.e0000 0001 2290 8069Laboratory of Hematology and Immunology & Laboratory for Myeloma Research, Vrije Universiteit Brussel (VUB) Belgium, Brussels, Belgium
| | - Hartmut Goldschmidt
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Stadlbauer
- grid.5330.50000 0001 2107 3311Department of Neurosurgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Erlangen, Germany ,grid.459693.4Institute of Medical Radiology, University Hospital St. Pölten, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Chunyan Sun
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Mei
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Martin Pecherstorfer
- grid.488547.2Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria
| | - Latifa Bakiri
- grid.22937.3d0000 0000 9259 8492Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria
| | - Erwin F. Wagner
- grid.22937.3d0000 0000 9259 8492Genes & Disease Group, Department of Dermatology, Medical University of Vienna (MUW), Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Genes & Disease Group, Department of Laboratory Medicine, Medical University of Vienna (MUW), Vienna, Austria
| | - Giovanni Tonon
- grid.18887.3e0000000417581884Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Scientific Institute, Milan, Italy ,grid.18887.3e0000000417581884Functional Genomics of Cancer Unit, Experimental Oncology Division, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martin Sattler
- grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA ,grid.62560.370000 0004 0378 8294Department of Surgery, Brigham and Women’s Hospital, Boston, MA USA
| | - Yu Hu
- grid.412839.50000 0004 1771 3250Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pierfrancesco Tassone
- grid.411489.10000 0001 2168 2547Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Dirk Jaeger
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany
| | - Klaus Podar
- grid.7700.00000 0001 2190 4373Department of Medical Oncology, National Center for Tumor Diseases (NCT), University of Heidelberg, Heidelberg, Germany ,grid.488547.2Department of Internal Medicine II, University Hospital Krems, Krems an der Donau, Austria ,grid.459693.4Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
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Gulla' A, Anderson KC. Multiple myeloma: the (r)evolution of current therapy and a glance into future. Haematologica 2020; 105:2358-2367. [PMID: 33054076 PMCID: PMC7556665 DOI: 10.3324/haematol.2020.247015] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past 20 years, the regulatory approval of several novel agents to treat multiple myeloma (MM) has prolonged median patient survival from 3 to 8-10 years. Increased understanding of MM biology has translated to advances in diagnosis, prognosis, and response assessment, as well as informed the development of targeted and immune agents. Here we provide an overview of the recent progress in MM, and highlight research areas of greatest promise to further improve patient outcome in the future.
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Affiliation(s)
| | - Kenneth C. Anderson
- Division of Hematologic Neoplasia, Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Clarisse D, Offner F, De Bosscher K. Latest perspectives on glucocorticoid-induced apoptosis and resistance in lymphoid malignancies. Biochim Biophys Acta Rev Cancer 2020; 1874:188430. [PMID: 32950642 DOI: 10.1016/j.bbcan.2020.188430] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/13/2020] [Accepted: 09/14/2020] [Indexed: 02/09/2023]
Abstract
Glucocorticoids are essential drugs in the treatment protocols of lymphoid malignancies. These steroidal hormones trigger apoptosis of the malignant cells by binding to the glucocorticoid receptor (GR), which is a member of the nuclear receptor superfamily. Long term glucocorticoid treatment is limited by two major problems: the development of glucocorticoid-related side effects, which hampers patient quality of life, and the emergence of glucocorticoid resistance, which is a gradual process that is inevitable in many patients. This emphasizes the need to reevaluate and optimize the widespread use of glucocorticoids in lymphoid malignancies. To achieve this goal, a deep understanding of the mechanisms governing glucocorticoid responsiveness is required, yet, a recent comprehensive overview is currently lacking. In this review, we examine how glucocorticoids mediate apoptosis by detailing GR's genomic and non-genomic action mechanisms in lymphoid malignancies. We continue with a discussion of the glucocorticoid-related problems and how these are intertwined with one another. We further zoom in on glucocorticoid resistance by critically analyzing the plethora of proposed mechanisms and highlighting therapeutic opportunities that emerge from these studies. In conclusion, early detection of glucocorticoid resistance in patients remains an important challenge as this would result in a timelier treatment reorientation and reduced glucocorticoid-instigated side effects.
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Affiliation(s)
- Dorien Clarisse
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Fritz Offner
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Karolien De Bosscher
- Translational Nuclear Receptor Research, VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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Lee LX, Li SC. Hunting down the dominating subclone of cancer stem cells as a potential new therapeutic target in multiple myeloma: An artificial intelligence perspective. World J Stem Cells 2020; 12:706-720. [PMID: 32952853 PMCID: PMC7477658 DOI: 10.4252/wjsc.v12.i8.706] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/08/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
The development of single-cell subclones, which can rapidly switch from dormant to dominant subclones, occur in the natural pathophysiology of multiple myeloma (MM) but is often "pressed" by the standard treatment of MM. These emerging subclones present a challenge, providing reservoirs for chemoresistant mutations. Technological advancement is required to track MM subclonal changes, as understanding MM's mechanism of evolution at the cellular level can prompt the development of new targeted ways of treating this disease. Current methods to study the evolution of subclones in MM rely on technologies capable of phenotypically and genotypically characterizing plasma cells, which include immunohistochemistry, flow cytometry, or cytogenetics. Still, all of these technologies may be limited by the sensitivity for picking up rare events. In contrast, more incisive methods such as RNA sequencing, comparative genomic hybridization, or whole-genome sequencing are not yet commonly used in clinical practice. Here we introduce the epidemiological diagnosis and prognosis of MM and review current methods for evaluating MM subclone evolution, such as minimal residual disease/multiparametric flow cytometry/next-generation sequencing, and their respective advantages and disadvantages. In addition, we propose our new single-cell method of evaluation to understand MM's mechanism of evolution at the molecular and cellular level and to prompt the development of new targeted ways of treating this disease, which has a broad prospect.
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Affiliation(s)
- Lisa X Lee
- Division of Hematology/Oncology, Department of Medicine, Chao Family Comprehensive Cancer Center, UCI Health, Orange, CA 92868, United States
| | - Shengwen Calvin Li
- Neuro-oncology and Stem Cell Research Laboratory, CHOC Children's Research Institute, Children's Hospital of Orange County, Orange, CA 92868, United States
- Department of Neurology, University of California-Irvine School of Medicine, Orange, CA 92868, United States
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35
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Vishnoi K, Viswakarma N, Rana A, Rana B. Transcription Factors in Cancer Development and Therapy. Cancers (Basel) 2020. [PMID: 32824207 DOI: 10.339/cancers12082296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer is a multi-step process and requires constitutive expression/activation of transcription factors (TFs) for growth and survival. Many of the TFs reported so far are critical for carcinogenesis. These include pro-inflammatory TFs, hypoxia-inducible factors (HIFs), cell proliferation and epithelial-mesenchymal transition (EMT)-controlling TFs, pluripotency TFs upregulated in cancer stem-like cells, and the nuclear receptors (NRs). Some of those, including HIFs, Myc, ETS-1, and β-catenin, are multifunctional and may regulate multiple other TFs involved in various pro-oncogenic events, including proliferation, survival, metabolism, invasion, and metastasis. High expression of some TFs is also correlated with poor prognosis and chemoresistance, constituting a significant challenge in cancer treatment. Considering the pivotal role of TFs in cancer, there is an urgent need to develop strategies targeting them. Targeting TFs, in combination with other chemotherapeutics, could emerge as a better strategy to target cancer. So far, targeting NRs have shown promising results in improving survival. In this review, we provide a comprehensive overview of the TFs that play a central role in cancer progression, which could be potential therapeutic candidates for developing specific inhibitors. Here, we also discuss the efforts made to target some of those TFs, including NRs.
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Affiliation(s)
- Kanchan Vishnoi
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Navin Viswakarma
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Ajay Rana
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA.,University of Illinois Hospital and Health Sciences System Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA.,Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Basabi Rana
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA.,University of Illinois Hospital and Health Sciences System Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA.,Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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36
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Vishnoi K, Viswakarma N, Rana A, Rana B. Transcription Factors in Cancer Development and Therapy. Cancers (Basel) 2020; 12:cancers12082296. [PMID: 32824207 PMCID: PMC7464564 DOI: 10.3390/cancers12082296] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is a multi-step process and requires constitutive expression/activation of transcription factors (TFs) for growth and survival. Many of the TFs reported so far are critical for carcinogenesis. These include pro-inflammatory TFs, hypoxia-inducible factors (HIFs), cell proliferation and epithelial-mesenchymal transition (EMT)-controlling TFs, pluripotency TFs upregulated in cancer stem-like cells, and the nuclear receptors (NRs). Some of those, including HIFs, Myc, ETS-1, and β-catenin, are multifunctional and may regulate multiple other TFs involved in various pro-oncogenic events, including proliferation, survival, metabolism, invasion, and metastasis. High expression of some TFs is also correlated with poor prognosis and chemoresistance, constituting a significant challenge in cancer treatment. Considering the pivotal role of TFs in cancer, there is an urgent need to develop strategies targeting them. Targeting TFs, in combination with other chemotherapeutics, could emerge as a better strategy to target cancer. So far, targeting NRs have shown promising results in improving survival. In this review, we provide a comprehensive overview of the TFs that play a central role in cancer progression, which could be potential therapeutic candidates for developing specific inhibitors. Here, we also discuss the efforts made to target some of those TFs, including NRs.
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Affiliation(s)
- Kanchan Vishnoi
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA; (K.V.); (N.V.); (A.R.)
| | - Navin Viswakarma
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA; (K.V.); (N.V.); (A.R.)
| | - Ajay Rana
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA; (K.V.); (N.V.); (A.R.)
- University of Illinois Hospital and Health Sciences System Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Basabi Rana
- Department of Surgery, Division of Surgical Oncology, University of Illinois at Chicago, Chicago, IL 60612, USA; (K.V.); (N.V.); (A.R.)
- University of Illinois Hospital and Health Sciences System Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Correspondence:
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Activating transcription factor 3 inhibits endometrial carcinoma aggressiveness via JunB suppression. Int J Oncol 2020; 57:707-720. [PMID: 32582999 PMCID: PMC7384851 DOI: 10.3892/ijo.2020.5084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023] Open
Abstract
The function of activating transcription factor 3 (ATF3) in cancer is context‑dependent and its role in endometrial carcinoma (EC) is yet to be elucidated. In the present study, ATF3 was indicated to be downregulated, while one of the ATF3‑interacting proteins, JunB, was upregulated in ECs according to western blot analysis. After overexpression in ECs, ATF3 inhibited the proliferation and invasion of EC cells and enhanced apoptosis, as well as suppressed the expression of JunB. The properties of EC cells, including the expression of matrix metalloproteinases, tissue inhibitors of metalloproteinases, the cell cycle and apoptosis were all altered by overexpression of ATF3. Furthermore, luciferase activity assay, chromatin precipitation and DNA affinity assay results indicated that ATF3 exerted the aforementioned functions via JunB binding and activator protein‑1 signaling. However, the interaction between ATF3 and JunB did not occur in EC cells under basal conditions, but in ATF3‑overexpressing ECs, which was capable of mitigating EC proliferation, invasion and metastasis. Collectively, the present results suggested that the ATF3/JunB interaction may serve as a potential therapeutic target for ECs.
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Johnston AD, Abdulrazak A, Sato H, Maqbool SB, Suzuki M, Greally JM, Simões-Pires CA. A Cellular Stress Response Induced by the CRISPR-dCas9 Activation System Is Not Heritable Through Cell Divisions. CRISPR J 2020; 3:188-197. [PMID: 33560917 DOI: 10.1089/crispr.2019.0077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The CRISPR-Cas9 system can be modified to perform "epigenetic editing" by utilizing the catalytically inactive (dead) Cas9 (dCas9) to recruit regulatory proteins to specific genomic locations. In prior studies, epigenetic editing with multimers of the transactivator VP16 and guide RNAs (gRNAs) was found to cause adverse cellular responses. These side effects may confound studies inducing new cellular properties, especially if the cellular responses are maintained through cell divisions-an epigenetic regulatory property. Here, we show how distinct components of this CRISPR-dCas9 activation system, particularly dCas9 with untargeted gRNAs, upregulate genes associated with transcriptional stress, defense response, and regulation of cell death. Our results highlight a previously undetected acute stress response to CRISPR-dCas9 components in human cells, which is transient and not maintained through cell divisions.
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Affiliation(s)
- Andrew D Johnston
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alali Abdulrazak
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hanae Sato
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Shahina B Maqbool
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Claudia A Simões-Pires
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
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Guan H, Peng R, Fang F, Mao L, Chen Z, Yang S, Dai C, Wu H, Wang C, Feng N, Xu B, Chen M. Tumor-associated macrophages promote prostate cancer progression via exosome-mediated miR-95 transfer. J Cell Physiol 2020; 235:9729-9742. [PMID: 32406953 DOI: 10.1002/jcp.29784] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/25/2020] [Accepted: 05/02/2020] [Indexed: 12/24/2022]
Abstract
Tumor-associated macrophages (TAMs) are vital constituents in mediating cell-to-cell communication within the tumor microenvironment. However, the molecular mechanisms underlying the interplay between TAMs and tumor cells that guide cell fate are largely undetermined. Extracellular vesicles, also known as exosomes, which are derived from TAMs, are the components exerting regulatory effects. Thus, understanding the underlying mechanism of "onco-vesicles" is of crucial importance for prostate cancer (PCa) therapy. In this study, we analyzed micro RNA sequences in exosomes released by THP-1 and M2 macrophages and found a significant increase in miR-95 levels in TAM-derived exosomes, demonstrating the direct uptake of miR-95 by recipient PCa cells. In vitro and in vivo loss-of-function assays suggested that miR-95 could function as a tumor promoter by directly binding to its downstream target gene, JunB, to promote PCa cell proliferation, invasion, and epithelial-mesenchymal transition. The clinical data analyses further revealed that higher miR-95 expression results in worse clinicopathological features. Collectively, our results demonstrated that TAM-mediated PCa progression is partially attributed to the aberrant expression of miR-95 in TAM-derived exosomes, and the miR-95/JunB axis provides the groundwork for research on TAMs to further develop more-personalized therapeutic approaches for patients with PCa.
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Affiliation(s)
- Han Guan
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Rui Peng
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Fang Fang
- Department of Immunology, School of Laboratory Medicine, Anhui Provincial Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, China
| | - Likai Mao
- Department of Urology, Second Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Zhijun Chen
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Shuai Yang
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Changyuan Dai
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Hongliang Wu
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Chengyong Wang
- Department of Urology, First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No.2 Hospital of Nanjing Medical University, Wuxi, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
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Yu T, Du C, Ma X, Sui W, Yu Z, Liu L, Zhao L, Li Z, Xu J, Wei X, Zhou W, Deng S, Zou D, An G, Tai YT, Tricot G, Anderson KC, Qiu L, Zhan F, Hao M. Polycomb-like Protein 3 Induces Proliferation and Drug Resistance in Multiple Myeloma and Is Regulated by miRNA-15a. Mol Cancer Res 2020; 18:1063-1073. [PMID: 32312841 DOI: 10.1158/1541-7786.mcr-19-0852] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/27/2019] [Accepted: 04/16/2020] [Indexed: 02/02/2023]
Abstract
Multiple myeloma remains incurable due to the persistence of a minor population of multiple myeloma cells that exhibit drug resistance, which leads to relapsed and/or refractory multiple myeloma. Elucidating the mechanism underlying drug resistance and developing an effective treatment are critical for clinical management of multiple myeloma. Here we showed that promoting expression of the gene for polycomb-like protein 3 (PHF19) induced multiple myeloma cell growth and multidrug resistance in vitro and in vivo. PHF19 was overexpressed in high-risk and drug-resistant primary cells from patients. High levels of PHF19 were correlated with inferior survival of patients with multiple myeloma, in the Total Therapy 2 cohort and in the Intergroup Francophone du Myeloma (IFM) cohort. Enhancing PHF19 expression levels increased Bcl-xL, Mcl-1, and HIF-1a expression in multiple myeloma cells. PHF19 also bound directly with EZH2 and promoted the phosphorylation of EZH2 through PDK1/AKT signaling. miR-15a is a small noncoding RNA that targeted the 3'UTR of PHF19. We found that downregulation of miR-15a led to high levels of PHF19 in multiple myeloma cells. These findings revealed that PHF19 served a crucial role in multiple myeloma proliferation and drug resistance and suggested that the miR-15a/PHF19/EZH2 pathway made a pivotal contribution to multiple myeloma pathogenesis, offering a promising approach to multiple myeloma treatment. IMPLICATIONS: Our findings identify that PHF19 mediates EZH2 phosphorylation as a mechanism of myeloma cell drug resistance, providing a rationale to explore therapeutic potential of targeting PHF19 in relapsed or refractory patients with multiple myeloma.
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Affiliation(s)
- Tengteng Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Chenxing Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaoke Ma
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Weiwei Sui
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Zhen Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lanting Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lei Zhao
- Department of Biophysics and Molecular Physiology, The University of Iowa, Roy J and Lucille A. Carver College of Medicine, Iowa City, Iowa
| | - Zhongqing Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jie Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaojing Wei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Wen Zhou
- Key Laboratory of Carcinogenesis, Ministry of Health, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, China
| | - Shuhui Deng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Dehui Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Gang An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yu-Tzu Tai
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Guido Tricot
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Fenghuang Zhan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Mu Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
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O'Flanagan CH, Campbell KR, Zhang AW, Kabeer F, Lim JLP, Biele J, Eirew P, Lai D, McPherson A, Kong E, Bates C, Borkowski K, Wiens M, Hewitson B, Hopkins J, Pham J, Ceglia N, Moore R, Mungall AJ, McAlpine JN, Shah SP, Aparicio S. Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses. Genome Biol 2019; 20:210. [PMID: 31623682 PMCID: PMC6796327 DOI: 10.1186/s13059-019-1830-0] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/10/2019] [Accepted: 09/20/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue microenvironments. However, the sources of technical and biological variation in primary solid tumor tissues and patient-derived mouse xenografts for scRNA-seq are not well understood. RESULTS We use low temperature (6 °C) protease and collagenase (37 °C) to identify the transcriptional signatures associated with tissue dissociation across a diverse scRNA-seq dataset comprising 155,165 cells from patient cancer tissues, patient-derived breast cancer xenografts, and cancer cell lines. We observe substantial variation in standard quality control metrics of cell viability across conditions and tissues. From the contrast between tissue protease dissociation at 37 °C or 6 °C, we observe that collagenase digestion results in a stress response. We derive a core gene set of 512 heat shock and stress response genes, including FOS and JUN, induced by collagenase (37 °C), which are minimized by dissociation with a cold active protease (6 °C). While induction of these genes was highly conserved across all cell types, cell type-specific responses to collagenase digestion were observed in patient tissues. CONCLUSIONS The method and conditions of tumor dissociation influence cell yield and transcriptome state and are both tissue- and cell-type dependent. Interpretation of stress pathway expression differences in cancer single-cell studies, including components of surface immune recognition such as MHC class I, may be especially confounded. We define a core set of 512 genes that can assist with the identification of such effects in dissociated scRNA-seq experiments.
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Affiliation(s)
- Ciara H O'Flanagan
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Kieran R Campbell
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
- UBC Data Science Institute, University of British Columbia, Vancouver, BC, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
- Graduate Bioinformatics program, University of British Columbia, Vancouver, BC, Canada
- BC Children's Hospital Research, Vancouver, BC, Canada
| | - Farhia Kabeer
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jamie L P Lim
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justina Biele
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Peter Eirew
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Daniel Lai
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Andrew McPherson
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Esther Kong
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Cherie Bates
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Kelly Borkowski
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Matt Wiens
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Brittany Hewitson
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - James Hopkins
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Jenifer Pham
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada
| | - Nicholas Ceglia
- Graduate Bioinformatics program, University of British Columbia, Vancouver, BC, Canada
| | - Richard Moore
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Jessica N McAlpine
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- UBC Data Science Institute, University of British Columbia, Vancouver, BC, Canada.
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Wang X, Fan H, Xu C, Jiang G, Wang H, Zhang J. KDM3B suppresses APL progression by restricting chromatin accessibility and facilitating the ATRA-mediated degradation of PML/RARα. Cancer Cell Int 2019; 19:256. [PMID: 31592194 PMCID: PMC6778369 DOI: 10.1186/s12935-019-0979-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/26/2019] [Indexed: 12/01/2022] Open
Abstract
Background A hallmark of acute promyelocytic leukemia (APL) is the expression of PML/RARα fusion protein. Treatment with all-trans retinoic acid (ATRA) results in the terminal differentiation of neutrophil granulocytes. However, the underlying mechanisms remain largely unknown. Here, we identify and elucidate a novel differentiation-suppressive model of APL involving the histone demethylase KDM3B, which has been identified as a suppressor of the tumor genes involved in hematopoietic malignancies. Methods First, we established a KDM3B knockdown NB4 cell model to determine the functional characteristics of KDM3B by cell proliferation assay and flow cytometry. Then, we performed ChIP-seq and ATAC-seq to search for potential relationships among KDM3B, histone modification (H3K9me1/me2) and the chromatin state. Finally, molecular biological techniques and a multi-omics analysis were used to explore the role of KDM3B in differentiation of the leukemia cells after ATRA treatment. Results We found that knocking down KDM3B contributed to the growth of NB4 APL cells via the promotion of cell-cycle progression and blocked granulocytic differentiation. Through global and molecular approaches, we provided futher evidence that knocking down KDM3B altered the global distribution of H3K9me1/me2 and increased the chromatin accessibility. Moreover, knocking down KDM3B inhibited the ATRA-induced degradation of the PML/RARα oncoprotein. Conclusion Our study suggested that KDM3B was able to inhibit APL progression by maintaining chromatin in a compact state and facilitating the ATRA-mediated degradation of PML/RARα. Taken together, the results show that KDM3B may be an alternative target for the treatment regimens and the targeted therapy for APL by sustaining the function of PML/RARα fusion protein.
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Affiliation(s)
- Xinrui Wang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Huiyong Fan
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Congling Xu
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Guojuan Jiang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Haiwei Wang
- 2Institute of Health Sciences, Shanghai Institutes for Biological Sciences and Graduate School, Chinese Academy of Sciences, Shanghai, 200025 China
| | - Ji Zhang
- 1State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
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Formononetin Regulates Multiple Oncogenic Signaling Cascades and Enhances Sensitivity to Bortezomib in a Multiple Myeloma Mouse Model. Biomolecules 2019; 9:biom9070262. [PMID: 31284669 PMCID: PMC6681380 DOI: 10.3390/biom9070262] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/30/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
Here, we determined the anti-neoplastic actions of formononetin (FT) against multiple myeloma (MM) and elucidated its possible mode of action. It was observed that FT enhanced the apoptosis caused by bortezomib (Bor) and mitigated proliferation in MM cells, and these events are regulated by nuclear factor-κB (NF-κB), phosphatidylinositol 3-kinase (PI3K)/AKT, and activator protein-1 (AP-1) activation. We further noted that FT treatment reduced the levels of diverse tumorigenic proteins involved in myeloma progression and survival. Interestingly, we observed that FT also blocked persistent NF-κB, PI3K/AKT, and AP-1 activation in myeloma cells. FT suppressed the activation of these oncogenic cascades by affecting a number of signaling molecules involved in their cellular regulation. In addition, FT augmented tumor growth-inhibitory potential of Bor in MM preclinical mouse model. Thus, FT can be employed with proteasomal inhibitors for myeloma therapy by regulating the activation of diverse oncogenic transcription factors involved in myeloma growth.
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He S, Sun H, Huang Y, Dong S, Qiao C, Zhang S, Wang C, Zheng F, Yan M, Yang G. Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2767512. [PMID: 31341891 PMCID: PMC6614972 DOI: 10.1155/2019/2767512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/14/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE MiRNAs have been widely analyzed in the occurrence and development of many diseases, including pterygium. This study aimed to identify the key genes and miRNAs in pterygium and to explore the underlying molecular mechanisms. METHODS MiRNA expression was initially extracted and pooled by published literature. Microarray data about differentially expressed genes was downloaded from Gene Expression Omnibus (GEO) database and analyzed with the R programming language. Functional and pathway enrichment analyses were performed using the database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction network was constructed with the STRING database. The associations between chemicals, differentially expressed miRNAs, and differentially expressed genes were predicted using the online resource. All the networks were constructed using Cytoscape. RESULTS We found that 35 miRNAs and 301 genes were significantly differentially expressed. Functional enrichment analysis showed that upregulated genes were significantly enriched in extracellular matrix (ECM) organization, while downregulated genes were mainly involved in cell death and apoptotic process. Finally, we concluded the chemical-gene affected network, miRNA-mRNA interacted networks, and significant pathway network. CONCLUSION We identified lists of differentially expressed miRNAs and genes and their possible interaction in pterygium. The networks indicated that ECM breakdown and EMT might be two major pathophysiological mechanisms and showed the potential significance of PI3K-Akt signalling pathway. MiR-29b-3p and collagen family (COL4A1 and COL3A1) might be new treatment target in pterygium.
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Affiliation(s)
- Siying He
- Center for Gene Diagnosis & Core Lab, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Hui Sun
- Center for Gene Diagnosis & Core Lab, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Yifang Huang
- Center for Gene Diagnosis & Core Lab, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Shiqi Dong
- Department of Ophthamology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Chen Qiao
- Department of Corneal, Hankou Aier Eye Hospital, Wuhan, Hubei 430024, China
| | - Shuai Zhang
- Center for Gene Diagnosis & Core Lab, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Chen Wang
- Center for Gene Diagnosis & Core Lab, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Fang Zheng
- Center for Gene Diagnosis & Core Lab, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
- Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, Hubei 430071, China
| | - Ming Yan
- Center for Gene Diagnosis & Core Lab, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
- Department of Ophthamology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Guohua Yang
- Demonstration Center for Experimental Basic Medicine Education of Wuhan University, Wuhan, Hubei 430071, China
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Li S, Vallet S, Sacco A, Roccaro A, Lentzsch S, Podar K. Targeting transcription factors in multiple myeloma: evolving therapeutic strategies. Expert Opin Investig Drugs 2019; 28:445-462. [DOI: 10.1080/13543784.2019.1605354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Shirong Li
- Division of Hematology/Oncology, Columbia University, New York, NY, USA
| | - Sonia Vallet
- Department of Internal Medicine II, University Hospital Krems, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Antonio Sacco
- Clinical Research Development and Phase I Unit, CREA Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Aldo Roccaro
- Clinical Research Development and Phase I Unit, CREA Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Suzanne Lentzsch
- Division of Hematology/Oncology, Columbia University, New York, NY, USA
| | - Klaus Podar
- Department of Internal Medicine II, University Hospital Krems, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
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Huang D, Petrykowska HM, Miller BF, Elnitski L, Ovcharenko I. Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression. Genome Res 2019; 29:657-667. [PMID: 30886051 PMCID: PMC6442386 DOI: 10.1101/gr.247007.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/14/2019] [Indexed: 12/22/2022]
Abstract
Compared to enhancers, silencers are notably difficult to identify and validate experimentally. In search for human silencers, we utilized H3K27me3-DNase I hypersensitive site (DHS) peaks with tissue specificity negatively correlated with the expression of nearby genes across 25 diverse cell lines. These regions are predicted to be silencers since they are physically linked, using Hi-C loops, or associated, using expression quantitative trait loci (eQTL) results, with a decrease in gene expression much more frequently than general H3K27me3-DHSs. Also, these regions are enriched for the binding sites of transcriptional repressors (such as CTCF, MECOM, SMAD4, and SNAI3) and depleted of the binding sites of transcriptional activators. Using sequence signatures of these regions, we constructed a computational model and predicted approximately 10,000 additional silencers per cell line and demonstrated that the majority of genes linked to these silencers are expressed at a decreased level. Furthermore, single nucleotide polymorphisms (SNPs) in predicted silencers are significantly associated with disease phenotypes. Finally, our results show that silencers commonly interact with enhancers to affect the transcriptional dynamics of tissue-specific genes and to facilitate fine-tuning of transcription in the human genome.
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Affiliation(s)
- Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hanna M Petrykowska
- Translational and Functional Genomics Branch, National Human Genome Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Brendan F Miller
- Translational and Functional Genomics Branch, National Human Genome Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
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Yen CH, Hsiao HH. NRF2 Is One of the Players Involved in Bone Marrow Mediated Drug Resistance in Multiple Myeloma. Int J Mol Sci 2018; 19:E3503. [PMID: 30405034 PMCID: PMC6274683 DOI: 10.3390/ijms19113503] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/28/2018] [Accepted: 11/04/2018] [Indexed: 02/07/2023] Open
Abstract
Multiple myeloma with clonal plasma expansion in bone marrow is the second most common hematologic malignancy in the world. Though the improvement of outcomes from the achievement of novel agents in recent decades, the disease progresses and leads to death eventually due to the elusive nature of myeloma cells and resistance mechanisms to therapeutic agents. In addition to the molecular and genetic basis of resistance pathomechanisms, the bone marrow microenvironment also contributes to disease progression and confers drug resistance in myeloma cells. In this review, we focus on the current state of the literature in terms of critical bone marrow microenvironment components, including soluble factors, cell adhesion mechanisms, and other cellular components. Transcriptional factor nuclear factor erythroid-derived-2-like 2 (NRF2), a central regulator for anti-oxidative stresses and detoxification, is implicated in chemoresistance in several cancers. The functional roles of NRF2 in myeloid-derived suppressor cells and multiple myeloma cells, and the potential of targeting NRF2 for overcoming microenvironment-mediated drug resistance in multiple myeloma are also discussed.
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Affiliation(s)
- Chia-Hung Yen
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan.
| | - Hui-Hua Hsiao
- Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan.
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
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Myeloma Bone Disease: Update on Pathogenesis and Novel Treatment Strategies. Pharmaceutics 2018; 10:pharmaceutics10040202. [PMID: 30355994 PMCID: PMC6321035 DOI: 10.3390/pharmaceutics10040202] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/15/2018] [Accepted: 10/20/2018] [Indexed: 01/31/2023] Open
Abstract
Bone disease, including osteolytic lesions and/or osteoporosis, is a common feature of multiple myeloma (MM). The consequences of skeletal involvement are severe pain, spinal cord compressions, and bone fractures, which have a dramatic impact on patients’ quality of life and, ultimately, survival. During the past few years, several landmark studies significantly enhanced our insight into MM bone disease (MBD) by identifying molecular mechanisms leading to increased bone resorption due to osteoclast activation, and decreased bone formation by osteoblast inhibition. Bisphosphonates were the mainstay to prevent skeletal-related events in MM for almost two decades. Excitingly, the most recent approval of the receptor activator of NF-kappa B ligand (RANKL) inhibitor, denosumab, expanded treatment options for MBD, for patients with compromised renal function, in particular. In addition, several other bone-targeting agents, including bone anabolic drugs, are currently in preclinical and early clinical assessment. This review summarizes our up-to-date knowledge on the pathogenesis of MBD and discusses novel state-of-the-art treatment strategies that are likely to enter clinical practice in the near future.
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Chai H, Liang Y, Wang S, Shen HW. A novel logistic regression model combining semi-supervised learning and active learning for disease classification. Sci Rep 2018; 8:13009. [PMID: 30158596 PMCID: PMC6115447 DOI: 10.1038/s41598-018-31395-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022] Open
Abstract
Traditional supervised learning classifier needs a lot of labeled samples to achieve good performance, however in many biological datasets there is only a small size of labeled samples and the remaining samples are unlabeled. Labeling these unlabeled samples manually is difficult or expensive. Technologies such as active learning and semi-supervised learning have been proposed to utilize the unlabeled samples for improving the model performance. However in active learning the model suffers from being short-sighted or biased and some manual workload is still needed. The semi-supervised learning methods are easy to be affected by the noisy samples. In this paper we propose a novel logistic regression model based on complementarity of active learning and semi-supervised learning, for utilizing the unlabeled samples with least cost to improve the disease classification accuracy. In addition to that, an update pseudo-labeled samples mechanism is designed to reduce the false pseudo-labeled samples. The experiment results show that this new model can achieve better performances compared the widely used semi-supervised learning and active learning methods in disease classification and gene selection.
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Affiliation(s)
- Hua Chai
- Faculty of Information Technology & State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, 999078, China
| | - Yong Liang
- Faculty of Information Technology & State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, 999078, China.
| | - Sai Wang
- Faculty of Information Technology & State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, 999078, China
| | - Hai-Wei Shen
- Faculty of Information Technology & State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, 999078, China
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Burwick N, Sharma S. Glucocorticoids in multiple myeloma: past, present, and future. Ann Hematol 2018; 98:19-28. [PMID: 30073393 DOI: 10.1007/s00277-018-3465-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/26/2018] [Indexed: 12/14/2022]
Abstract
Glucocorticoids are a backbone of treatment for multiple myeloma in both the upfront and relapsed/refractory setting. While glucocorticoids have single agent activity in multiple myeloma, in the modern era, they are paired with novel agents to induce high clinical response rates. On the other hand, toxicities of steroid therapy limit high dose delivery and impact patient quality of life. We provide a history of steroid use in multiple myeloma with the aim to understand how steroids have emerged and persisted in the treatment of multiple myeloma. We review mechanisms of glucocorticoid sensitivity and resistance and highlight potential future directions to evaluate steroid responsiveness. Further research in this area will aid in optimizing steroid utilization and help determine when glucocorticoid therapy may no longer benefit patients.
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Affiliation(s)
- Nicholas Burwick
- VA Puget Sound Health Care System, Seattle, WA, USA. .,Department of Medicine, University of Washington, 1705 NE Pacific St, M/S 358280, Seattle, WA, 98195, USA.
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