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Adhikary S, Singh V, Choudhari R, Yang B, Adhikari S, Ramos EI, Chaudhuri S, Roy S, Gadad SS, Das C. ZMYND8 suppresses MAPT213 LncRNA transcription to promote neuronal differentiation. Cell Death Dis 2022; 13:766. [PMID: 36064715 PMCID: PMC9445031 DOI: 10.1038/s41419-022-05212-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 01/21/2023]
Abstract
Zinc Finger transcription factors are crucial in modulating various cellular processes, including differentiation. Chromatin reader Zinc Finger MYND (Myeloid, Nervy, and DEAF-1) type containing 8 (ZMYND8), an All-Trans Retinoic Acid (ATRA)-responsive gene, was previously shown to play a crucial role in promoting the expression of neuronal-lineage committed genes. Here, we report that ZMYND8 promotes neuronal differentiation by positively regulating canonical MAPT protein-coding gene isoform, a key player in the axonal development of neurons. Additionally, ZMYND8 modulates gene-isoform switching by epigenetically silencing key regulatory regions within the MAPT gene, thereby suppressing the expression of non-protein-coding isoforms such as MAPT213. Genetic deletion of ZMYND8 led to an increase in the MAPT213 that potentially suppressed the parental MAPT protein-coding transcript expression related to neuronal differentiation programs. In addition, ectopic expression of MAPT213 led to repression of MAPT protein-coding transcript. Similarly, ZMYND8-driven transcription regulation was also observed in other neuronal differentiation-promoting genes. Collectively our results elucidate a novel mechanism of ZMYND8-dependent transcription regulation of different neuronal lineage committing genes, including MAPT, to promote neural differentiation.
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Affiliation(s)
- Santanu Adhikary
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.417635.20000 0001 2216 5074Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India
| | - Vipin Singh
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.450257.10000 0004 1775 9822Homi Bhaba National Institute, Mumbai, 400094 India
| | - Ramesh Choudhari
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Barbara Yang
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Swagata Adhikari
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.450257.10000 0004 1775 9822Homi Bhaba National Institute, Mumbai, 400094 India
| | - Enrique I. Ramos
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA
| | - Soumi Chaudhuri
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India
| | - Siddhartha Roy
- grid.417635.20000 0001 2216 5074Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India
| | - Shrikanth S. Gadad
- grid.449768.0Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, 5001 El Paso Drive, El Paso, TX 79905 USA ,grid.267309.90000 0001 0629 5880Mays Cancer Center, UT Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229 USA
| | - Chandrima Das
- grid.473481.d0000 0001 0661 8707Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India ,grid.450257.10000 0004 1775 9822Homi Bhaba National Institute, Mumbai, 400094 India
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2
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Mondal P, Tiwary N, Sengupta A, Dhang S, Roy S, Das C. Epigenetic Reprogramming of the Glucose Metabolic Pathways by the Chromatin Effectors During Cancer. Subcell Biochem 2022; 100:269-336. [PMID: 36301498 DOI: 10.1007/978-3-031-07634-3_9] [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] [Indexed: 06/16/2023]
Abstract
Glucose metabolism plays a vital role in regulating cellular homeostasis as it acts as the central axis for energy metabolism, alteration in which may lead to serious consequences like metabolic disorders to life-threatening diseases like cancer. Malignant cells, on the other hand, help in tumor progression through abrupt cell proliferation by adapting to the changed metabolic milieu. Metabolic intermediates also vary from normal cells to cancerous ones to help the tumor manifestation. However, metabolic reprogramming is an important phenomenon of cells through which they try to maintain the balance between normal and carcinogenic outcomes. In this process, transcription factors and chromatin modifiers play an essential role to modify the chromatin landscape of important genes related directly or indirectly to metabolism. Our chapter surmises the importance of glucose metabolism and the role of metabolic intermediates in the cell. Also, we summarize the influence of histone effectors in reprogramming the cancer cell metabolism. An interesting aspect of this chapter includes the detailed methods to detect the aberrant metabolic flux, which can be instrumental for the therapeutic regimen of cancer.
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Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Niharika Tiwary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Sinjini Dhang
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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3
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Validation of ZMYND8 as a new treatment target in hepatocellular carcinoma. J Cancer Res Clin Oncol 2021; 147:3517-3534. [PMID: 34462784 DOI: 10.1007/s00432-021-03768-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/14/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND ZMYND8 (Zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8) has been known to play an important role in tumor regulation in various types of cancer. However, the results of ZMYND8 expression and their clinical significance in hepatocellular carcinoma (HCC) have not yet been published. In the present study, we investigate the expression of ZMYND8 protein and mRNA in HCC and elucidate its prognostic significance. METHODS ZMYND8 protein and mRNA expression in 283 and 234 HCCs were investigated using immunohistochemistry and microarray gene expression profiling data. The relationships between ZMYND8 expression with clinicopathologic features and prognosis of HCC patients were evaluated. Furthermore, we performed the invasion, migration, apoptosis, soft agar formation assay and sphere formation assay in HCC cell lines, and evaluated tumorigenicity in a nude mouse model, after ZMYND8 knockdown. RESULTS Overexpression of ZMYND8 protein and mRNA was observed in 20.5% and 26.9% of HCC cases, respectively. High ZMYND8 expression showed significant correlations with microvascular invasion, high Edmondson grade, advanced American Joint Committee on Cancer, and increased alpha-fetoprotein level. ZMYND8 mRNA overexpression was an independent prognostic factor for predicting early recurrence as well as short recurrence-free survival (RFS). Downregulation of ZMYND8 reduced migration and invasion of HCC cells, and promoted apoptosis of HCC cells in an in vitro model. In a xenograft nude mouse model, knockdown of ZMYND8 significantly reduced tumor growth. CONCLUSION ZMYND8 mRNA overexpression could be a prognostic marker of shorter RFS in HCC patients after curative resection. ZMYND8 might play an important role in the proliferation and progression of HCC and could be a promising candidate for targeted therapy.
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ZMYND8-regulated IRF8 transcription axis is an acute myeloid leukemia dependency. Mol Cell 2021; 81:3604-3622.e10. [PMID: 34358447 DOI: 10.1016/j.molcel.2021.07.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023]
Abstract
The transformed state in acute leukemia requires gene regulatory programs involving transcription factors and chromatin modulators. Here, we uncover an IRF8-MEF2D transcriptional circuit as an acute myeloid leukemia (AML)-biased dependency. We discover and characterize the mechanism by which the chromatin "reader" ZMYND8 directly activates IRF8 in parallel with the MYC proto-oncogene through their lineage-specific enhancers. ZMYND8 is essential for AML proliferation in vitro and in vivo and associates with MYC and IRF8 enhancer elements that we define in cell lines and in patient samples. ZMYND8 occupancy at IRF8 and MYC enhancers requires BRD4, a transcription coactivator also necessary for AML proliferation. We show that ZMYND8 binds to the ET domain of BRD4 via its chromatin reader cassette, which in turn is required for proper chromatin occupancy and maintenance of leukemic growth in vivo. Our results rationalize ZMYND8 as a potential therapeutic target for modulating essential transcriptional programs in AML.
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5
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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Karmakar D, Maity J, Mondal P, Shyam Chowdhury P, Sikdar N, Karmakar P, Das C, Sengupta S. E2F5 promotes prostate cancer cell migration and invasion through regulation of TFPI2, MMP-2 and MMP-9. Carcinogenesis 2021; 41:1767-1780. [PMID: 32386317 DOI: 10.1093/carcin/bgaa043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
Previously, our laboratory demonstrated that a deregulated E2F5/p38/SMAD3 axis was associated with uncontrolled cellular proliferation in prostate cancer (PCa). Here, we investigate the role of E2F5 in PCa in further details. RNAi-mediated E2F5 knockdown and pathway-focused gene expression profiling in PC3 cells identified TFPI2 as a downstream target of E2F5. Manipulation of E2F5 expression was also found to alter MMP-2 and MMP-9 levels as detected by Proteome Profiler array, western blot and reverse transcription coupled quantitative polymerase chain reaction Site-directed mutagenesis, dual-luciferase assays and chromatin immunoprecipitation with anti-E2F5-IgG coupled with qPCR confirmed recruitment of E2F5 on TFPI2, MMP-2 and MMP-9 promoters. RNAi-mediated knockdown of E2F5 expression in PC3 caused a significant alteration of cell migration while that of TFFI2 resulted in a modest change. Abrogation of E2F5 and TFPI2 expression was associated with significant changes in the gelatinolytic activity of active forms of MMP-2 and MMP-9. Moreover, E2F5, MMP-2 and MMP-9 levels were elevated in biopsies of PCa patients relative to that of benign hyperplasia, while TFPI2 expression was reduced. MMP-9 was coimmunoprecipitated with anti-TFPI2-IgG in PCa tissue samples suggesting a direct interaction between the proteins. Finally, artemisinin treatment in PC3 cells repressed E2F5 along with MMP-2/MMP-9 while triggering TFPI2 expression which alleviated PC3 aggressiveness possibly through inhibition of MMP activities. Together, our study reinstates an oncogenic role of E2F5 which operates as a dual-function transcription factor for its targets TFPI2, MMP-2 and MMP-9 and promotes cellular invasiveness. This study also indicates a therapeutic potential of artemisinin, a natural compound which acts by correcting dysfunctional E2F5/TFPI2/MMP axis in PCa.
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Affiliation(s)
- Deepmala Karmakar
- Department of Biochemistry, University of Calcutta, Kolkata, West Bengal, India
| | - Jyotirindra Maity
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Department of Life Sciences, Homi Bhaba National Institute (HBNI), BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, India
| | - Puskar Shyam Chowdhury
- Department of Urology, K. P. C. Medical College and Hospital Campus, Jadavpur, Kolkata, West Bengal, India
| | - Nilabja Sikdar
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, West Bengal, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, West Bengal, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Department of Life Sciences, Homi Bhaba National Institute (HBNI), BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, India
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7
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Regulation of ZMYND8 to Treat Cancer. Molecules 2021; 26:molecules26041083. [PMID: 33670804 PMCID: PMC7923094 DOI: 10.3390/molecules26041083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
Abstract
Zinc finger myeloid, nervy, and deformed epidermal autoregulatory factor 1-type containing 8 (Zinc finger MYND-type containing 8, ZMYND8) is a transcription factor, a histone H3-interacting protein, and a putative chromatin reader/effector that plays an essential role in regulating transcription during normal cellular growth. Mutations and altered expression of ZMYND8 are associated with the development and progression of cancer. Increased expression of ZMYND8 is linked to breast, prostate, colorectal, and cervical cancers. It exerts pro-oncogenic effects in breast and prostate cancers, and it promotes angiogenesis in zebrafish, as well as in breast and prostate cancers. In contrast, downregulation of ZMYND8 is also reported in breast, prostate, and nasopharyngeal cancers. ZMYND8 acts as a tumor suppressor in breast and prostate cancers, and it inhibits tumor growth by promoting differentiation; inhibiting proliferation, cell-cycle progression, invasiveness, and metastasis; and maintaining the epithelial phenotype in various types of cancers. These data together suggest that ZMYND8 is important in tumorigenesis; however, the existing data are contradictory. More studies are necessary to clarify the exact role of ZMYND8 in tumorigenesis. In the future, regulation of expression/activity of ZMYND8 and/or its binding partners may become useful in treating cancer.
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8
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Dou C, Mo H, Chen T, Liu J, Zeng Y, Li S, Guo C, Zhang C. ZMYND8 promotes the growth and metastasis of hepatocellular carcinoma by promoting HK2-mediated glycolysis. Pathol Res Pract 2021; 219:153345. [PMID: 33517164 DOI: 10.1016/j.prp.2021.153345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
The bromodomain protein zinc finger MYND-type containing 8 (ZMYND8) plays a critical role in human breast cancer. However, the expression and biological function of ZMYND8 in hepatocellular carcinoma (HCC) are poorly understood. In this study, ZMYND8 expression was found to be elevated in HCC based on the cancer genome atlas (TCGA) and gene expression omnibus (GEO) databases. Next, we confirmed that ZMYND8 was frequently overexpressed in HCC tissues compared with adjacent non-tumor tissues. The up-regulated level of ZMYND8 was also observed in HCC cell lines. Elevated ZMYND8 expression was correlated with unfavorable clinicopathological features and poor prognosis of HCC patients. Functionally, ectopic expression of ZMYND8 potentiated the proliferation, migration, and invasion of Hep3B cells. Conversely, ZMYND8 knockdown led to the reduced proliferation and invasiveness of HCCLM3 cells. ZMYND8 silencing restrained the growth of HCCLM3 cells in vivo. Mechanistically, ZMYND8 enhanced glucose consumption, lactate production, and ATP level in HCC cells. Pharmacological inhibition of glycolysis using 2-DG blocked the promoting effects of ZMYND8 on HCC cell proliferation and mobility. Furthermore, hexokinase 2 (HK2), a key enzyme of glycolysis, was identified as the downstream target of ZMYND8 in HCC cells. ZMYND8 promoted HK2 transcription by recruiting bromodomain containing 4 (BRD4) to its promoter. Knockdown of HK2 abrogated the oncogenic functions of ZMYND8 in HCC. Altogether, these data indicated that ZMYND8 promoted the growth and metastasis of HCC by promoting HK2-mediated glycolysis and might serve as a promising biomarker and therapeutic target for HCC.
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Affiliation(s)
- Changwei Dou
- Department of Hepatopancreatobiliary Surgery & Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
| | - Huanye Mo
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Tianxiang Chen
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Jie Liu
- Department of Hepatopancreatobiliary Surgery & Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
| | - Yuqun Zeng
- Department of Nephrology, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang Province 310014, China.
| | - Shuangshuang Li
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
| | - Cheng Guo
- Department of Hepatobiliary Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Chengwu Zhang
- Department of Hepatopancreatobiliary Surgery & Minimally Invasive Surgery, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, 310014, China.
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9
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Mukherjee S, Adhikary S, Gadad SS, Mondal P, Sen S, Choudhari R, Singh V, Adhikari S, Mandal P, Chaudhuri S, Sengupta A, Lakshmanaswamy R, Chakrabarti P, Roy S, Das C. Suppression of poised oncogenes by ZMYND8 promotes chemo-sensitization. Cell Death Dis 2020; 11:1073. [PMID: 33323928 PMCID: PMC7738522 DOI: 10.1038/s41419-020-03129-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
The major challenge in chemotherapy lies in the gain of therapeutic resistance properties of cancer cells. The relatively small fraction of chemo-resistant cancer cells outgrows and are responsible for tumor relapse, with acquired invasiveness and stemness. We demonstrate that zinc-finger MYND type-8 (ZMYND8), a putative chromatin reader, suppresses stemness, drug resistance, and tumor-promoting genes, which are hallmarks of cancer. Reinstating ZMYND8 suppresses chemotherapeutic drug doxorubicin-induced tumorigenic potential (at a sublethal dose) and drug resistance, thereby resetting the transcriptional program of cells to the epithelial state. The ability of ZMYND8 to chemo-sensitize doxorubicin-treated metastatic breast cancer cells by downregulating tumor-associated genes was further confirmed by transcriptome analysis. Interestingly, we observed that ZMYND8 overexpression in doxorubicin-treated cells stimulated those involved in a good prognosis in breast cancer. Consistently, sensitizing the cancer cells with ZMYND8 followed by doxorubicin treatment led to tumor regression in vivo and revert back the phenotypes associated with drug resistance and stemness. Intriguingly, ZMYND8 modulates the bivalent or poised oncogenes through its association with KDM5C and EZH2, thereby chemo-sensitizing the cells to chemotherapy for better disease-free survival. Collectively, our findings indicate that poised chromatin is instrumental for the acquisition of chemo-resistance by cancer cells and propose ZMYND8 as a suitable epigenetic tool that can re-sensitize the chemo-refractory breast carcinoma.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinogenesis/drug effects
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Line, Tumor
- Cell Movement/drug effects
- Cell Movement/genetics
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Doxorubicin/pharmacology
- Doxorubicin/therapeutic use
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
- Epigenesis, Genetic/drug effects
- Epithelial-Mesenchymal Transition/drug effects
- Epithelial-Mesenchymal Transition/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Genome, Human
- Histone Demethylases/metabolism
- Humans
- Mice, Inbred BALB C
- Mice, Nude
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogenes
- Phenotype
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Treatment Outcome
- Triple Negative Breast Neoplasms/drug therapy
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/pathology
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Shrikanth S Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynaecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Sabyasachi Sen
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Ramesh Choudhari
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Shri B. M. Patil Medical College, Hospital and Research Centre, BLDE (Deemed to be University), Vijayapura, Karnataka, 586103, India
| | - Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Pratiti Mandal
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Soumi Chaudhuri
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
| | - Rajkumar Lakshmanaswamy
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, 79905, USA
| | - Partha Chakrabarti
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Homi Bhaba National Institute, Mumbai, India.
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10
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A novel role of tumor suppressor ZMYND8 in inducing differentiation of breast cancer cells through its dual-histone binding function. J Biosci 2020. [DOI: 10.1007/s12038-019-9980-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Mondal P, Sen S, Klein BJ, Tiwary N, Gadad SS, Kutateladze TG, Roy S, Das C. TCF19 Promotes Cell Proliferation through Binding to the Histone H3K4me3 Mark. Biochemistry 2020; 59:389-399. [PMID: 31746185 PMCID: PMC11540549 DOI: 10.1021/acs.biochem.9b00771] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Transcription factor 19 (TCF19) plays critical roles in type 1 diabetes and the maintenance of pancreatic β cells. Recent studies have also implicated TCF19 in cell proliferation of hepatic carcinoma and non-small cell lung carcinoma; however, the mechanism underlying this regulation remains elusive. At the molecular level, TCF19 contains two modules, the plant homeodomain (PHD) finger and the forkhead-associated (FHA) domain, of unclear function. Here, we show that TCF19 mediates hepatocellular carcinoma HepG2 cell proliferation through its PHD finger that recognizes trimethylated lysine 4 of histone 3 (H3K4me3). W316 of the PHD finger of TCF19 is one of the critical residues eliciting this function. Whole genome microarray analysis and orthogonal cell-based assays identified a large subset of genes involved in cell survival and proliferation that depend on TCF19. Our data suggest that TCF19 acts as a pro-oncogene in hepatocellular carcinoma cells and that its functional PHD finger is critical in cell proliferation.
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Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Sabyasachi Sen
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Brianna J. Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Niharika Tiwary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
| | - Shrikanth S. Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Texas Tech University Health Sciences Center, El Paso, Texas 79905, United States
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhaba National Institute, Mumbai 400094, India
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12
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Chen J, He Q, Wu P, Fu J, Xiao Y, Chen K, Xie D, Zhang X. ZMYND8 expression combined with pN and pM classification as a novel prognostic prediction model for colorectal cancer: Based on TCGA and GEO database analysis. Cancer Biomark 2020; 28:201-211. [PMID: 32224527 DOI: 10.3233/cbm-191261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8 (ZMYND8) is closely correlated with tumor proliferation and invasiveness. However, its prognostic value has not been estimated in colorectal cancer (CRC). OBJECTIVE We aimed to elucidate the prognostic significance of ZMYND8 expression and the pN and pM classification supplemented by its expression in CRCs. METHODS The candidate gene ZMYND8 is identified by TCGA database and GEO database, and then we retrospectively evaluated the status and prognostic significance of ZMYND8 expression of 174 patients with CRC. RESULTS Online data showed high expression of ZMYND8 is closely correlated with worse overall survival. Our study revealed high expression of ZMYND8 in CRC patients was significantly associated with worse overall and disease-free survival (P< 0.05), and was an independently adverse prognostic factor for overall survival (P< 0.001) and disease-free survival (P= 0.001) by univariate and multivariate analysis. C-index to combined prognostic model containing the pN, pM classification supplemented by the status of ZMYND8 expression showed improved predictive ability comparing with the pN and pM classification model (C-index of 0.597 vs. 0.545, respectively). CONCLUSION The combined prognostic model could improve the ability to determine the clinical outcome of patients with CRC.
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Affiliation(s)
- Jiewei Chen
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Qingmei He
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Peishan Wu
- Department of Pathology, The Second Affiliated Hospital of Shantou University Medical College, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jianchang Fu
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yongbo Xiao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Keming Chen
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Dan Xie
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xinke Zhang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Guangdong Esophageal Cancer Institute, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
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13
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Chen J, Liu J, Chen X, Li Y, Li Z, Shen C, Chen K, Zhang X. Low expression of ZMYND8 correlates with aggressive features and poor prognosis in nasopharyngeal carcinoma. Cancer Manag Res 2019; 11:7835-7843. [PMID: 31692588 PMCID: PMC6713802 DOI: 10.2147/cmar.s210305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/04/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose ZMYND8 is closely correlated with cancerous proliferation and invasiveness. However, its prognostic value has not been estimated in a nasopharyngeal carcinoma (NPC). The purpose of this study was to elucidate the status of ZMYND8 expression and its prognostic significance in NPCs. Methods The status of ZMYND8 expression was investigated by immunohistochemistry for NPC samples in the study. The cutoff value of ZMYND8 expression was confirmed in NPCs using ROC-curve analysis. Correlations between ZMYND8 expression and clinicopathological variables and patient prognosis were analyzed by various statistical methods. Results Our study showed that low expression of ZMYND8 strongly correlated with late T stage in NPCs (P<0.05). Kaplan–Meier survival analysis revealed a significant association between low ZMYND8 expression and worse overall survival (P<0.05). Most importantly, Cox regression analysis confirmed ZMYND8 expression in NPC could be an independent prognostic factor. Conclusion Low expression of ZMYND8 could be of importance, due to its displaying more aggressive behavior in NPC. Therefore, ZMYND8 expression might serve as an independent prediction factor in patients with NPCs.
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Affiliation(s)
- Jiewei Chen
- 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, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Jun 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, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Xiaoting Chen
- 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, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Yong Li
- 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, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Zizi Li
- Department of Pathology, Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, People's Republic of China
| | - Chengchao Shen
- 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, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Keming Chen
- 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, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Xinke 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, Guangzhou, 510060, People's Republic of China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
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14
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Miller MD, Salinas EA, Newtson AM, Sharma D, Keeney ME, Warrier A, Smith BJ, Bender DP, Goodheart MJ, Thiel KW, Devor EJ, Leslie KK, Gonzalez-Bosquet J. An integrated prediction model of recurrence in endometrial endometrioid cancers. Cancer Manag Res 2019; 11:5301-5315. [PMID: 31239780 PMCID: PMC6559142 DOI: 10.2147/cmar.s202628] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/22/2019] [Indexed: 02/03/2023] Open
Abstract
Objectives: Endometrial cancer incidence and mortality are rising in the US. Disease recurrence has been shown to have a significant impact on mortality. However, to date, there are no accurate and validated prediction models that would discriminate which individual patients are likely to recur. Reliably predicting recurrence would be of benefit for treatment decisions following surgery. We present an integrated model constructed with comprehensive clinical, pathological and molecular features designed to discriminate risk of recurrence for patients with endometrioid endometrial adenocarcinoma. Subjects and methods: A cohort of endometrioid endometrial cancer patients treated at our institution was assembled. Clinical characteristics were extracted from patient charts. Primary tumors from these patients were obtained and total tissue RNA extracted for RNA sequencing. A prediction model was designed containing both clinical characteristics and molecular profiling of the tumors. The same analysis was carried out with data derived from The Cancer Genome Atlas for replication and external validation. Results: Prediction models derived from our institutional data predicted recurrence with high accuracy as evidenced by areas under the curve approaching 1. Similar trends were observed in the analysis of TCGA data. Further, a scoring system for risk of recurrence was devised that showed specificities as high as 81% and negative predictive value as high as 90%. Lastly, we identify specific molecular characteristics of patient tumors that may contribute to the process of disease recurrence. Conclusion: By constructing a comprehensive model, we are able to reliably predict recurrence in endometrioid endometrial cancer. We devised a clinically useful scoring system and thresholds to discriminate risk of recurrence. Finally, the data presented here open a window to understanding the mechanisms of recurrence in endometrial cancer.
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Affiliation(s)
- Marina D Miller
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Erin A Salinas
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Andreea M Newtson
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Deepti Sharma
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Matthew E Keeney
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Akshaya Warrier
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Brian J Smith
- Department of Biostatistics, University of Iowa College of Public Health, Iowa City, IA, USA
| | - David P Bender
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Michael J Goodheart
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Kristina W Thiel
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Eric J Devor
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Kimberly K Leslie
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Jesus Gonzalez-Bosquet
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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15
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Jin X, Xu XE, Jiang YZ, Liu YR, Sun W, Guo YJ, Ren YX, Zuo WJ, Hu X, Huang SL, Shen HJ, Lan F, He YF, Hu GH, Di GH, He XH, Li DQ, Liu S, Yu KD, Shao ZM. The endogenous retrovirus-derived long noncoding RNA TROJAN promotes triple-negative breast cancer progression via ZMYND8 degradation. SCIENCE ADVANCES 2019; 5:eaat9820. [PMID: 30854423 PMCID: PMC6402854 DOI: 10.1126/sciadv.aat9820] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 01/23/2019] [Indexed: 05/03/2023]
Abstract
Human endogenous retroviruses (HERVs) play pivotal roles in the development of breast cancer. However, the detailed mechanisms of noncoding HERVs remain elusive. Here, our genome-wide transcriptome analysis of HERVs revealed that a primate long noncoding RNA, which we dubbed TROJAN, was highly expressed in human triple-negative breast cancer (TNBC). TROJAN promoted TNBC proliferation and invasion and indicated poor patient outcomes. We further confirmed that TROJAN could bind to ZMYND8, a metastasis-repressing factor, and increase its degradation through the ubiquitin-proteasome pathway by repelling ZNF592. TROJAN also epigenetically up-regulated metastasis-related genes in multiple cell lines. Correlations between TROJAN and ZMYND8 were subsequently confirmed in clinical samples. Furthermore, our study verified that antisense oligonucleotide therapy targeting TROJAN substantially suppressed TNBC progression in vivo. In conclusion, the long noncoding RNA TROJAN promotes TNBC progression and serves as a potential therapeutic target.
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Affiliation(s)
- Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Xiao-En Xu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Corresponding author. (Z.-M.S.); (X.-E.X.); (K.-D.Y.); (S.L.)
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Yi-Rong Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Wei Sun
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Ya-Jie Guo
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Yi-Xing Ren
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Wen-Jia Zuo
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Xin Hu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Sheng-Lin Huang
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Hong-Jie Shen
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Fei Lan
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Yun-Fei He
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Guo-Hong Hu
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Gen-Hong Di
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
| | - Xiang-Huo He
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Da-Qiang Li
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Suling Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
- Corresponding author. (Z.-M.S.); (X.-E.X.); (K.-D.Y.); (S.L.)
| | - Ke-Da Yu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Corresponding author. (Z.-M.S.); (X.-E.X.); (K.-D.Y.); (S.L.)
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Cancer Institute, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong-An Road, Shanghai 200032, P. R. China
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai 200032, P. R. China
- Corresponding author. (Z.-M.S.); (X.-E.X.); (K.-D.Y.); (S.L.)
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16
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Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai JA, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon KR, Pękowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Di Virgilio M. The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination. Mol Cell 2018; 72:636-649.e8. [PMID: 30293785 PMCID: PMC6242708 DOI: 10.1016/j.molcel.2018.08.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/01/2018] [Accepted: 08/25/2018] [Indexed: 01/18/2023]
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector component of antibody responses. CSR is initiated by activation-induced cytidine deaminase (AID), which targets transcriptionally active immunoglobulin heavy chain (Igh) switch donor and acceptor DNA. The 3′ Igh super-enhancer, 3′ regulatory region (3′RR), is essential for acceptor region transcription, but how this function is regulated is unknown. Here, we identify the chromatin reader ZMYND8 as an essential regulator of the 3′RR. In B cells, ZMYND8 binds promoters and super-enhancers, including the Igh enhancers. ZMYND8 controls the 3′RR activity by modulating the enhancer transcriptional status. In its absence, there is increased 3′RR polymerase loading and decreased acceptor region transcription and CSR. In addition to CSR, ZMYND8 deficiency impairs somatic hypermutation (SHM) of Igh, which is also dependent on the 3′RR. Thus, ZMYND8 controls Igh diversification in mature B lymphocytes by regulating the activity of the 3′ Igh super-enhancer. ZMYND8 is required for GLT of acceptor S regions and Class Switch Recombination ZMYND8 supports efficient somatic hypermutation of the Igh variable regions ZMYND8 binds B cell super-enhancers, including the 3′ Igh enhancer ZMYND8 modulates the transcriptional status and activity of the 3′ Igh enhancer
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Affiliation(s)
- Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Daniel B Rosen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joy A Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Lisa Keller
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | | | | | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Madlen Driesner
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Roman I Subbotin
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NCI, NIH, Bethesda, MD 20892, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, The Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
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Abstract
Our genetic information is organized into chromatin, which consists of histones and proteins involved in regulating DNA compaction, accessibility and function. Chromatin is decorated by histone modifications, which provide signals that coordinate DNA-based processes including transcription and DNA damage response (DDR) pathways. A major signal involved in these processes is acetylation, which when attached to lysines within proteins, including histones, can be recognized and read by bromodomain-containing proteins. We recently identified the bromodomain protein ZMYND8 (also known as RACK7 and PRKCBP1) as a critical DNA damage response factor involved in regulating transcriptional responses and DNA repair activities at DNA double-strand breaks. Other studies have further defined the molecular details for how ZMYND8 interacts with chromatin and other chromatin modifying proteins to exert its DNA damage response functions. ZMYND8 also plays essential roles in regulating transcription during normal cellular growth, perturbation of which promotes cellular processes involved in cancer initiation and progression. In addition to acetylation, histone methylation and demethylase enzymes have emerged as important regulators of ZMYND8. Here we discuss our current understanding of the molecular mechanisms that govern ZMYND8 function within chromatin, highlighting the importance of this protein for genome maintenance both during the DDR and in cancer.
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Affiliation(s)
- Fade Gong
- a Department of Molecular Biosciences, Institute for Cellular and Molecular Biology , The University of Texas at Austin , 2506 Speedway, Austin , TX 78712 , USA
| | - Kyle M Miller
- a Department of Molecular Biosciences, Institute for Cellular and Molecular Biology , The University of Texas at Austin , 2506 Speedway, Austin , TX 78712 , USA
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Profiling of the transcriptional response to all-trans retinoic acid in breast cancer cells reveals RARE-independent mechanisms of gene expression. Sci Rep 2017; 7:16684. [PMID: 29192143 PMCID: PMC5709375 DOI: 10.1038/s41598-017-16687-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/15/2017] [Indexed: 12/15/2022] Open
Abstract
Retinoids, derivatives of vitamin A, are key physiological molecules with regulatory effects on cell differentiation, proliferation and apoptosis. As a result, they are of interest for cancer therapy. Specifically, models of breast cancer have varied responses to manipulations of retinoid signaling. This study characterizes the transcriptional response of MDA-MB-231 and MDA-MB-468 breast cancer cells to retinaldehyde dehydrogenase 1A3 (ALDH1A3) and all-trans retinoic acid (atRA). We demonstrate limited overlap between ALDH1A3-induced gene expression and atRA-induced gene expression in both cell lines, suggesting that the function of ALDH1A3 in breast cancer progression extends beyond its role as a retinaldehyde dehydrogenase. Our data reveals divergent transcriptional responses to atRA, which are largely independent of genomic retinoic acid response elements (RAREs) and consistent with the opposing responses of MDA-MB-231 and MDA-MB-468 to in vivo atRA treatment. We identify transcription factors associated with each gene set. Manipulation of the IRF1 transcription factor demonstrates that it is the level of atRA-inducible and epigenetically regulated transcription factors that determine expression of target genes (e.g. CTSS, cathepsin S). This study provides a paradigm for complex responses of breast cancer models to atRA treatment, and illustrates the need to characterize RARE-independent responses to atRA in a variety of models.
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Dual histone reader ZMYND8 inhibits cancer cell invasion by positively regulating epithelial genes. Biochem J 2017; 474:1919-1934. [DOI: 10.1042/bcj20170223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/19/2017] [Accepted: 04/21/2017] [Indexed: 01/28/2023]
Abstract
Enhanced migratory potential and invasiveness of cancer cells contribute crucially to cancer progression. These phenotypes are achieved by precise alteration of invasion-associated genes through local epigenetic modifications which are recognized by a class of proteins termed a chromatin reader. ZMYND8 [zinc finger MYND (myeloid, Nervy and DEAF-1)-type containing 8], a key component of the transcription regulatory network, has recently been shown to be a novel reader of H3.1K36Me2/H4K16Ac marks. Through differential gene expression analysis upon silencing this chromatin reader, we identified a subset of genes involved in cell proliferation and invasion/migration regulated by ZMYND8. Detailed analysis uncovered its antiproliferative activity through BrdU incorporation, alteration in the expression of proliferation markers, and cell cycle regulating genes and cell viability assays. In addition, performing wound healing and invasion/migration assays, its anti-invasive nature is evident. Interestingly, epithelial–mesenchymal transition (EMT), a key mechanism of cellular invasion, is regulated by ZMYND8 where we identified its selective enrichment on promoters of CLDN1/CDH1 genes, rich in H3K36Me2/H4K16Ac marks, leading to their up-regulation. Thus, the presence of ZMYND8 could be implicated in maintaining the epithelial phenotype of cells. Furthermore, syngeneic mice, injected with ZMYND8-overexpressed invasive breast cancer cells, showed reduction in tumor volume and weight. In concert with this, we observed a significant down-regulation of ZMYND8 in invasive ductal and lobular breast cancer tissues compared with normal tissue. Taken together, our study elucidates a novel function of ZMYND8 in regulating EMT and invasion of cancer cells, possibly through its chromatin reader function.
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