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Zhou Y, Yu H, Zhang D, Wang Z, Li Q, An X, Zhang S, Li Z. Imprinted lncRNA KCNQ1OT1 regulates CDKN1C expression through promoter binding and chromatin folding in pigs. Gene 2024; 923:148590. [PMID: 38772516 DOI: 10.1016/j.gene.2024.148590] [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: 02/22/2024] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024]
Abstract
Long noncoding RNAs (lncRNAs) are implicated in a number of regulatory functions in eukaryotic genomes. In humans, KCNQ1OT1 is a 91 kb imprinted lncRNA that inhibits multiple surrounding genes in cis. Among them, CDKN1C is closely related to KCNQ1OT1 and is involved in multiple epigenetic disorders. Here, we found that pigs also had a relatively conserved paternal allele expressing KCNQ1OT1 and had a shorter 5' end (∼27 kb) compared to human KCNQ1OT1. Knockdown of KCNQ1OT1 using antisense oligonucleotides (ASO) showed that upregulation of CDKN1C expression in pigs. However, porcine KCNQ1OT1 did not affect the DNA methylation status of the CpG islands in the promoters of KCNQ1OT1 and CDKN1C. Inhibition of DNA methyltransferase using Decitabine treatment resulted in a significant increase in both KCNQ1OT1 and CDKN1C expression, suggesting that the regulation between KCNQ1OT1 and CDKN1C may not be dependent on RNA interference. Further use of chromosome conformation capture and reverse transcription-associated trap detection in the region where CDKN1C was located revealed that KCNQ1OT1 bound to the CDKN1C promoter and affected chromosome folding. Phenotypically, inhibition of KCNQ1OT1 at the cumulus-oocyte complex promoted cumulus cell transformation, and to upregulated the expression of ALPL at the early stage of osteogenic differentiation of porcine bone marrow mesenchymal stem cells. Our results confirm that the expression of KCNQ1OT1 imprinting in pigs as well as porcine KCNQ1OT1 regulates the expression of CDKN1C through direct promoter binding and chromatin folding alteration. And this regulatory mechanism played an important role in cell differentiation.
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Affiliation(s)
- Yongfeng Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, China
| | - Daoyu Zhang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Zhengzhu Wang
- Shenzhen University Affiliated South China Hospital, Shenzhen, China
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China.
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2
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Zhu Y, Yan Z, Fu C, Wen X, Jia L, Zhou L, Du Z, Wang C, Wang Y, Chen J, Nie Y, Wang W, Cui J, Wang G, Hoffman AR, Hu JF, Li W. LncRNA Osilr9 coordinates promoter DNA demethylation and the intrachromosomal loop structure required for maintaining stem cell pluripotency. Mol Ther 2023; 31:1791-1806. [PMID: 36523163 PMCID: PMC10278046 DOI: 10.1016/j.ymthe.2022.12.010] [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: 01/03/2020] [Revised: 06/08/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Nuclear reprogramming of somatic cells into a pluripotent status has the potential to create patient-specific induced pluripotent stem cells for regenerative medicine. Currently, however, the epigenetic mechanisms underlying this pluripotent reprogramming are poorly understood. To delineate this epigenetic regulatory network, we utilized a chromatin RNA in situ reverse transcription sequencing (CRIST-seq) approach to identify long noncoding RNAs (lncRNAs) embedded in the 3-dimensional intrachromosomal architecture of stem cell core factor genes. By combining CRIST-seq and RNA sequencing, we identified Oct4-Sox2 interacting lncRNA 9 (Osilr9) as a pluripotency-associated lncRNA. Osilr9 expression was associated with the status of stem cell pluripotency in reprogramming. Using short hairpin RNA (shRNA) knockdown, we showed that this lncRNA was required for the optimal maintenance of stem cell pluripotency. Overexpression of Osilr9 induced robust activation of endogenous stem cell core factor genes in fibroblasts. Osilr9 participated in the formation of the intrachromosomal looping required for the maintenance of pluripotency. After binding to the Oct4 promoter, Osilr9 recruited the DNA demethylase ten-eleven translocation 1, leading to promoter demethylation. These data demonstrate that Osilr9 is a critical chromatin epigenetic modulator that coordinates the promoter activity of core stem cell factor genes, highlighting the critical role of pluripotency-associated lncRNAs in stem cell pluripotency and reprogramming.
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Affiliation(s)
- Yanbo Zhu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Zi Yan
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun 130021, Jilin, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Changhao Fu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jingcheng Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yuanyuan Nie
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Wenjun Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
| | - Guixia Wang
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun 130021, Jilin, China.
| | - Andrew R Hoffman
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
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Nandi S, Mondal A, Ghosh A, Mukherjee S, Das C. Lnc-ing epigenetic mechanisms with autophagy and cancer drug resistance. Adv Cancer Res 2023; 160:133-203. [PMID: 37704287 DOI: 10.1016/bs.acr.2023.03.002] [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: 09/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) comprise a diverse class of RNA molecules that regulate various physiological processes and have been reported to be involved in several human pathologies ranging from neurodegenerative disease to cancer. Therapeutic resistance is a major hurdle for cancer treatment. Over the past decade, several studies has emerged on the role of lncRNAs in cancer drug resistance and many trials have been conducted employing them. LncRNAs also regulate different cell death pathways thereby maintaining a fine balance of cell survival and death. Autophagy is a complex cell-killing mechanism that has both cytoprotective and cytotoxic roles. Similarly, autophagy can lead to the induction of both chemosensitization and chemoresistance in cancer cells upon therapeutic intervention. Recently the role of lncRNAs in the regulation of autophagy has also surfaced. Thus, lncRNAs can be used in cancer therapeutics to alleviate the challenges of chemoresistance by targeting the autophagosomal axis. In this chapter, we discuss about the role of lncRNAs in autophagy-mediated cancer drug resistance and its implication in targeted cancer therapy.
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Affiliation(s)
- Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Aritra Ghosh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Indian Institute of Science Education and Research, Kolkata, India
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India.
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4
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Diagnostic and prognostic value of the RUNXOR/RUNX1 axis in multiple sclerosis. Neurobiol Dis 2023; 178:106032. [PMID: 36754216 DOI: 10.1016/j.nbd.2023.106032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
The runt-related transcription factor-1 (RUNX1) gene with its lncRNA RUNXOR are recently becoming a research focus in various diseases, specifically immune-related diseases as they are implicated in multiple pathways. Interestingly, their role in multiple sclerosis (MS) remains unstudied. The present study explored the role of RUNXOR/RUNX1 in the development and progression of MS and investigated their possible mechanism of action. We measured the serum expression levels of lncRNA RUNXOR, as well as RUNX1, microtubule associated protein 2 (MAP2), nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) mRNAs in 30 healthy controls and 120 MS patients subdivided into 4 groups: 30 clinically isolated syndrome patients, 30 relapsing-remitting MS (RRMS) patients in relapse, 30 RRMS patients in remission and 30 secondary progressive MS patients. Additionally, we measured the serum protein levels of RUNX1, MAP2, NGF, BDNF and interleukin-10 (IL-10). All measured RNA expression levels were markedly downregulated and, consequently, the protein levels of RUNX1, MAP2, NGF, BDNF and IL-10 were significantly decreased in MS patients compared to healthy controls. Moreover, the levels of the measured parameters varied significantly within the MS groups. According to receiver-operating-characteristic (ROC) curve and logistic regression analyses, lncRNA RUNXOR, RUNX1 mRNA and its protein levels were predictors of disease progression, in addition to RUNX1 mRNA exhibiting a diagnostic potential. Altogether, this study suggests the implication of the RUNXOR-RUNX1 axis in MS development, progression, and increased MS-related disability, and highlights the potential utility of the studied parameters as promising diagnostic/prognostic biomarkers for MS.
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5
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Liu Y, Han Y, Zhang Y, Lv T, Peng X, Huang J. LncRNAs has been identified as regulators of Myeloid-derived suppressor cells in lung cancer. Front Immunol 2023; 14:1067520. [PMID: 36817434 PMCID: PMC9932034 DOI: 10.3389/fimmu.2023.1067520] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Lung tumours are widespread pathological conditions that attract much attention due to their high incidence of death. The immune system contributes to the progression of these diseases, especially non-small cell lung cancer, resulting in the fast evolution of immune-targeted therapy. Myeloid-derived suppressor cells (MDSCs) have been suggested to promote the progression of cancer in the lungs by suppressing the immune response through various mechanisms. Herein, we summarized the clinical studies on lung cancer related to MDSCs. However, it is noteworthy to mention the discovery of long non-coding RNAs (lncRNAs) that had different phenotypes and could regulate MDSCs in lung cancer. Therefore, by reviewing the different phenotypes of lncRNAs and their regulation on MDSCs, we summarized the lncRNAs' impact on the progression of lung tumours. Data highlight LncRNAs as anti-cancer agents. Hence, we aim to discuss their possibilities to inhibit tumour growth and trigger the development of immunosuppressive factors such as MDSCs in lung cancer through the regulation of lncRNAs. The ultimate purpose is to propose novel and efficient therapy methods for curing patients with lung tumours.
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Affiliation(s)
- Yifan Liu
- Department of Oncology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei, China.,Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
| | - Yukun Han
- Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China.,Department of Medical Imaging, School of Medicine, and Positron Emission Computed Tomography (PET) Center of the First Affiliated Hospital, Yangtze University, Jingzhou, Hubei, China
| | - Yanhua Zhang
- Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
| | - Tongtong Lv
- Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
| | - Xiaochun Peng
- Department of Pathophysiology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei, China
| | - Jinbai Huang
- Department of Medical Imaging, School of Medicine, and Positron Emission Computed Tomography (PET) Center of the First Affiliated Hospital, Yangtze University, Jingzhou, Hubei, China
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6
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Abstract
OPINION STATEMENT Acute myeloid leukemia (AML) is the most common form of leukemia in adults, leading to the highest number of annual leukemia-associated deaths in the USA. Although most AML patients initially enter remission following induction therapy, most eventually relapse, underscoring the unmet need for more effective therapies. In recent years, novel high-throughput sequencing techniques, and mouse and human models of disease have increased our understanding of the molecular mechanisms that lead to AML. Leukemogenic mechanisms can be broadly classified into two types-cell-intrinsic and cell-extrinsic. Cell-intrinsic mechanisms include an array of genetic and epigenetic alterations that lead to dysregulated gene expression and function in hematopoietic stem/progenitor cells, leading to their increased fitness and ultimately, malignant transformation. Extrinsic mechanisms include both hematopoietic and non-hematopoietic stromal components of the leukemic microenvironment that interact with pre-leukemic and leukemic clones to promote their survival, self-renewal, and/or resistance to therapy. Through the individual and concerted action of these factors, pre-leukemic clones acquire the changes necessary for leukemic transformation. In addition, following therapy, specific leukemic clones are selected for that eventually re-initiate disease. Improving our understanding of these cell-intrinsic and cell-extrinsic mechanisms will provide novel opportunities to treat AML as well as prevent the development of disease.
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7
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HULC targets the IGF1R-PI3K-AKT axis in trans to promote breast cancer metastasis and cisplatin resistance. Cancer Lett 2022; 548:215861. [PMID: 35981570 DOI: 10.1016/j.canlet.2022.215861] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 12/11/2022]
Abstract
Insulin-like growth factor I receptor (IGF1R) is frequently upregulated in breast cancer. Due to its intrinsic tyrosine kinase activity, aberrant activation of the IGF1R signaling axis may enhance tumor cell proliferation and cancer stemness, causing tumor relapse, metastasis and resistance to chemotherapy. We utilized a chromatin RNA in situ reverse transcription (CRIST) approach to characterize molecular factors that regulate the IGF1R network. We identified lncRNA HULC (Highly Upregulated in Liver Cancer) as a key trans-regulator of IGF1R in breast cancer cells. Loss of HULC suppressed the expression of IGF1R and the activation of its downstream PI3K/AKT pathway, while HULC overexpression activated the axis in breast cancer cells. Using a transcription-associated trap (RAT) assay, we demonstrated that HULC functioned as a nuclear lncRNA and epigenetically activated IGF1R by directly binding to the intragenic regulatory elements of the gene, orchestrating intrachromosomal interactions, and promoting histone H3K9 acetylation. The activated HULC-IGF1R/PI3K/AKT pathway mediated tumor resistance to cisplatin through the increased expression of cancer stemness markers, including NANOG, SOX2, OCT4, CD44 and ALDH1A1. In immunodeficient mice, stimulation of the HULC-IGF1R pathway promoted tumor metastasis. These data suggest that HULC may be a new epigenetic target for IGF1R axis-targeted therapeutic intervention.
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8
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Wang Y, Jia L, Wang C, Du Z, Zhang S, Zhou L, Wen X, Li H, Chen H, Nie Y, Li D, Liu S, Figueroa DS, Ay F, Xu W, Zhang S, Li W, Cui J, Hoffman AR, Guo H, Hu JF. Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. J Cell Biol 2022; 221:213009. [PMID: 35171230 PMCID: PMC8855478 DOI: 10.1083/jcb.202009134] [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: 09/24/2020] [Revised: 12/01/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
The molecular circuitry that causes stem cells to exit from pluripotency remains largely uncharacterized. Using chromatin RNA in situ reverse transcription sequencing, we identified Peln1 as a novel chromatin RNA component in the promoter complex of Oct4, a stem cell master transcription factor gene. Peln1 was negatively associated with pluripotent status during somatic reprogramming. Peln1 overexpression caused E14 cells to exit from pluripotency, while Peln1 downregulation induced robust reprogramming. Mechanistically, we discovered that Peln1 interacted with the Oct4 promoter and recruited the DNA methyltransferase DNMT3A. By de novo altering the epigenotype in the Oct4 promoter, Peln1 dismantled the intrachromosomal loop that is required for the maintenance of pluripotency. Using RNA reverse transcription-associated trap sequencing, we showed that Peln1 targets multiple pathway genes that are associated with stem cell self-renewal. These findings demonstrate that Peln1 can act as a new epigenetic player and use a trans mechanism to induce an exit from the pluripotent state in stem cells.
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Affiliation(s)
- Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Zhonghua Du
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Xue Wen
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Li
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Yuanyuan Nie
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | | | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Andrew R Hoffman
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Guo
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
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9
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Park SJ, Nam DE, Seong HC, Hahn YS. New Discovery of Myeloid-Derived Suppressor Cell's Tale on Viral Infection and COVID-19. Front Immunol 2022; 13:842535. [PMID: 35185933 PMCID: PMC8850309 DOI: 10.3389/fimmu.2022.842535] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/17/2022] [Indexed: 01/08/2023] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are generated under biological stress such as cancer, inflammatory tissue damage, and viral infection. In recent years, with occurrence of global infectious diseases, new discovery on MDSCs functions has been significantly expanded during viral infection and COVID-19. For a successful viral infection, pathogens viruses develop immune evasion strategies to avoid immune recognition. Numerous viruses induce the differentiation and expansion of MDSCs in order to suppress host immune responses including natural killer cells, antigen presenting cells, and T-cells. Moreover, MDSCs play an important role in regulation of immunopathogenesis by balancing viral infection and tissue damage. In this review article, we describe the overview of immunomodulation and genetic regulation of MDSCs during viral infection in the animal model and human studies. In addition, we include up-to-date review of role of MDSCs in SARS-CoV-2 infection and COVID-19. Finally, we discuss potential therapeutics targeting MDSCs.
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Affiliation(s)
- Soo-Jeung Park
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
| | - Da-eun Nam
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
| | - Hae Chang Seong
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
| | - Young S. Hahn
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, United States
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, United States
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10
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Zhong F, Yao F, Cheng Y, Liu J, Zhang N, Li S, Li M, Huang B, Wang X. m6A-related lncRNAs predict prognosis and indicate immune microenvironment in acute myeloid leukemia. Sci Rep 2022; 12:1759. [PMID: 35110624 PMCID: PMC8810799 DOI: 10.1038/s41598-022-05797-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex hematologic malignancy. Survival rate of AML patients is low. N6-methyladenosine (m6A) and long non-coding RNAs (lncRNAs) play important roles in AML tumorigenesis and progression. However, the relationship between lncRNAs and biological characteristics of AML, as well as how lncRNAs influence the prognosis of AML patients, remain unclear. In this study. In this study, Pearson correlation analysis was used to identify lncRNAs related to m6A regulatory genes, namely m6A-related lncRNAs. And we analyzed their roles and prognostic values in AML. m6A-related lncRNAs associated with patient prognosis were screened using univariate Cox regression analysis, followed by systematic analysis of the relationship between these genes and AML clinicopathologic and biologic characteristics. Furthermore, we examined the characteristics of tumor immune microenvironment (TIME) using different IncRNA clustering models. Using LASSO regression, we identified the risk signals related to prognosis of AML patients. We then constructed and verified a risk model based on m6A-related lncRNAs for independent prediction of overall survival in AML patients. Our results indicate that risk scores, calculated based on risk-related signaling, were related to the clinicopathologic characteristics of AML and level of immune infiltration. Finally, we examined the expression level of TRAF3IP2-AS1 in patient samples through real-time polymerase chain reaction analysis and in GEO datasets, and we identified a interaction relationship between SRSF10 and TRAF3IP2-AS1 through in vitro assays. Our study shows that m6A-related lncRNAs, evaluated using the risk prediction model, can potentially be used to predict prognosis and design immunotherapy in AML patients.
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Affiliation(s)
- Fangmin Zhong
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China.,School of Public Health, Nanchang University, No. 461 BaYi Boulevard, Nanchang, 330006, Jiangxi, China
| | - Fangyi Yao
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Ying Cheng
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Jing Liu
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Nan Zhang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Shuqi Li
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Meiyong Li
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China
| | - Bo Huang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China. .,School of Public Health, Nanchang University, No. 461 BaYi Boulevard, Nanchang, 330006, Jiangxi, China.
| | - Xiaozhong Wang
- Jiangxi Province Key Laboratory of Laboratory Medicine, Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China. .,School of Public Health, Nanchang University, No. 461 BaYi Boulevard, Nanchang, 330006, Jiangxi, China.
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11
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Chai P, Jia R, Li Y, Zhou C, Gu X, Yang L, Shi H, Tian H, Lin H, Yu J, Zhuang A, Ge S, Jia R, Fan X. Regulation of epigenetic homeostasis in uveal melanoma and retinoblastoma. Prog Retin Eye Res 2021; 89:101030. [PMID: 34861419 DOI: 10.1016/j.preteyeres.2021.101030] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
Uveal melanoma (UM) and retinoblastoma (RB), which cause blindness and even death, are the most frequently observed primary intraocular malignancies in adults and children, respectively. Epigenetic studies have shown that changes in the epigenome contribute to the rapid progression of both UM and RB following classic genetic changes. The loss of epigenetic homeostasis plays an important role in oncogenesis by disrupting the normal patterns of gene expression. The targetable nature of epigenetic modifications provides a unique opportunity to optimize treatment paradigms and establish new therapeutic options for both UM and RB with these aberrant epigenetic modifications. We aimed to review the research findings regarding relevant epigenetic changes in UM and RB. Herein, we 1) summarize the literature, with an emphasis on epigenetic alterations, including DNA methylation, histone modifications, RNA modifications, noncoding RNAs and an abnormal chromosomal architecture; 2) elaborate on the regulatory role of epigenetic modifications in biological processes during tumorigenesis; and 3) propose promising therapeutic candidates for epigenetic targets and update the list of epigenetic drugs for the treatment of UM and RB. In summary, we endeavour to depict the epigenetic landscape of primary intraocular malignancy tumorigenesis and provide potential epigenetic targets in the treatment of these tumours.
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Affiliation(s)
- Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ruobing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Yongyun Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Chuandi Zhou
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Hanhan Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Hao Tian
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Huimin Lin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Jie Yu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, PR China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, PR China.
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12
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Kirtonia A, Ashrafizadeh M, Zarrabi A, Hushmandi K, Zabolian A, Bejandi AK, Rani R, Pandey AK, Baligar P, Kumar V, Das BC, Garg M. Long noncoding RNAs: A novel insight in the leukemogenesis and drug resistance in acute myeloid leukemia. J Cell Physiol 2021; 237:450-465. [PMID: 34569616 DOI: 10.1002/jcp.30590] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/10/2021] [Accepted: 09/01/2021] [Indexed: 12/19/2022]
Abstract
Acute myeloid leukemia (AML) is a common hematological disorder with heterogeneous nature that resulted from blocked myeloid differentiation and an enhanced number of immature myeloid progenitors. During several decades, different factors, including cytogenetic, genetic, and epigenetic have been reported to contribute to the pathogenesis of AML by inhibiting the differentiation and ensuring the proliferation of myeloid blast cells. Recently, long noncoding RNAs (lncRNAs) have been considered as potential diagnostic, therapeutic, and prognostic factors in different human malignancies including AML. Altered expression of lncRNAs is correlated with the transformation of hematopoietic stem and progenitor cells into leukemic blast cells because of their distinct role in the key cellular processes. We discuss the significant role of lncRNAs in the proliferation, survival, differentiation, leukemic stem cells in AML and their involvement in different molecular pathways (insulin-like growth factor type I receptor, FLT3, c-KIT, Wnt, phosphatidylinositol 3-kinase/protein kinase-B, microRNAs), and associated mechanisms such as autophagy, apoptosis, and glucose metabolism. In addition, we aim to highlight the role of lncRNAs as reliable biomarkers for diagnosis, prognosis, and drug resistance for precision medicine in AML.
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Affiliation(s)
- Anuradha Kirtonia
- Amity Institute of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | - Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Tuzla, Istanbul, Turkey.,Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul, Turkey
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul, Turkey.,Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Sariyer, Istanbul, Turkey
| | - Kiavash Hushmandi
- Division of Epidemiology and Zoonoses, Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Amirhossein Zabolian
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Atefe K Bejandi
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Reshma Rani
- Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, India
| | - Amit K Pandey
- Amity Institute of Biotechnology (AIB), Amity University, Gurgaon, Haryana, India
| | - Prakash Baligar
- Amity Institute of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | - Bhudev C Das
- Amity Institute of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
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13
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Dysregulation of lncRNA in Helicobacter pylori-Infected Gastric Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6911734. [PMID: 34337048 PMCID: PMC8286195 DOI: 10.1155/2021/6911734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori (H. pylori) infection is the most common cause of gastric cancer (GC). This microorganism is genetically diverse; GC is caused by several genetic deregulations in addition to environmental factors and bacterial virulence factors. lncRNAs (long noncoding RNAs) are significant biological macromolecules in GC, have specific functions in diseases, and could be therapeutic targets. Altered lncRNAs can lead to the abnormal expression of adjacent protein-coding genes, which may be important in cancer development. Their mechanisms have not been well understood, so we are going to investigate the risk of GC in a population with both high lncRNA and H. pylori infection.
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14
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Farooqi AA, Gulnara K, Mukhanbetzhanovna AA, Datkhayev U, Kussainov AZ, Adylova A. Regulation of RUNX proteins by long non-coding RNAs and circular RNAs in different cancers. Noncoding RNA Res 2021; 6:100-106. [PMID: 34189363 PMCID: PMC8209647 DOI: 10.1016/j.ncrna.2021.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/05/2021] [Accepted: 05/25/2021] [Indexed: 12/27/2022] Open
Abstract
RUNX proteins have been shown to behave as "double-edge sword" in wide variety of cancers. Discovery of non-coding RNAs has played linchpin role in improving our understanding about the post-transcriptional regulation of different cell signaling pathways. Several new mechanistic insights and distinct modes of cross-regulation of RUNX proteins and non-coding RNAs have been highlighted by recent research. In this review we have attempted to provide an intricate interplay between non-coding RNAs and RUNX proteins in different cancers. Better conceptual and mechanistic understanding of layered regulation of RUNX proteins by non-coding RNAs will be helpful in effective translation of the laboratory findings to clinically effective therapeutics.
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Affiliation(s)
| | - Kapanova Gulnara
- Al-Farabi Kazakh National University, 71 Al-Farabi Avenue, Almaty, 050040, Kazakhstan
| | | | - Ubaidilla Datkhayev
- Asfendiyarov Kazakh National Medical University, KazNMU, Tole Bi St 94, Almaty, 050000, Kazakhstan
| | - Abay Z Kussainov
- Kazakh National Medical University Named After S. D. Asfendiyarov, Kazakhstan
| | - Aima Adylova
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
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15
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Zhang J, Thakuri BKC, Zhao J, Nguyen LN, Nguyen LNT, Khanal S, Cao D, Dang X, Schank M, Lu Z, Wu XY, Morrison ZD, El Gazzar M, Jiang Y, Ning S, Wang L, Moorman JP, Yao ZQ. Long Noncoding RNA RUNXOR Promotes Myeloid-Derived Suppressor Cell Expansion and Functions via Enhancing Immunosuppressive Molecule Expressions during Latent HIV Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 206:2052-2060. [PMID: 33820854 DOI: 10.4049/jimmunol.2001008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
RUNX1 overlapping RNA (RUNXOR) is a long noncoding RNA and a key regulator of myeloid-derived suppressor cells (MDSCs) via targeting runt-related transcription factor 1 (RUNX1). We and others have previously reported MDSC expansion and inhibition of host immune responses during viral infections; however, the mechanisms regulating MDSC differentiation and suppressive functions, especially the role of RUNXOR-RUNX1 in the regulation of MDSCs in people living with HIV (PLHIV), remain unknown. In this study, we demonstrate that RUNXOR and RUNX1 expressions are upregulated in MDSCs that expand and accumulate in human PBMCs derived from PLHIV. We found that the upregulation of RUNXOR and RUNX1 is associated with the expressions of several key immunosuppressive molecules, including arginase 1, inducible NO synthase, STAT3, IL-6, and reactive oxygen species. RUNXOR and RUNX1 could positively regulate each other's expression and control the expressions of these suppressive mediators. Specifically, silencing RUNXOR or RUNX1 expression in MDSCs from PLHIV attenuated MDSC expansion and immunosuppressive mediator expressions, whereas overexpressing RUNXOR in CD33+ myeloid precursors from healthy subjects promoted their differentiation into MDSCs and enhanced the expression of these mediators. Moreover, loss of RUNXOR-RUNX1 function in MDSCs improved IFN-γ production from cocultured autologous CD4 T cells derived from PLHIV. These results suggest that the RUNXOR-RUNX1 axis promotes the differentiation and suppressive functions of MDSCs via regulating multiple immunosuppressive signaling molecules and may represent a potential target for immunotherapy in conjunction with antiviral therapy in PLHIV.
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Affiliation(s)
- Jinyu Zhang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Bal Krishna Chand Thakuri
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Juan Zhao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Lam N Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Lam N T Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Sushant Khanal
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Dechao Cao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Xindi Dang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Madison Schank
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Zeyuan Lu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Xiao Y Wu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Zheng D Morrison
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Mohamed El Gazzar
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Yong Jiang
- Department of Biomedical Sciences, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN; and
| | - Shunbin Ning
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Ling Wang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN
| | - Jonathan P Moorman
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Department of Veterans Affairs, Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Johnson City, TN
| | - Zhi Q Yao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN; .,Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN.,Department of Veterans Affairs, Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Johnson City, TN
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16
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Gao X, Sui H, Zhao S, Gao X, Su Y, Qu P. Immunotherapy Targeting Myeloid-Derived Suppressor Cells (MDSCs) in Tumor Microenvironment. Front Immunol 2021; 11:585214. [PMID: 33613512 PMCID: PMC7889583 DOI: 10.3389/fimmu.2020.585214] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of immature myeloid cells that accumulate in tumor-bearing hosts to reduce T cells activity and promote tumor immune escape in the tumor microenvironment (TME). The immune system in the TME can be stimulated to elicit an anti-tumor immune response through immunotherapy. The main theory of immunotherapy resides on the plasticity of the immune system and its capacity to be re-educated into a potent anti-tumor response. Thus, MDSCs within the TME became one of the major targets to improve the efficacy of tumor immunotherapy, and therapeutic strategies for tumor MDSCs were developed in the last few years. In the article, we analyzed the function of tumor MDSCs and the regulatory mechanisms of agents targeting MDSCs in tumor immunotherapy, and reviewed their therapeutic effects in MDSCs within the TME. Those data focused on discussing how to promote the differentiation and maturation of MDSCs, reduce the accumulation and expansion of MDSCs, and inhibit the function, migration and recruitment of MDSCs, further preventing the growth, invasion and metastasis of tumor. Those investigations may provide new directions for cancer therapy.
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Affiliation(s)
- Xidan Gao
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Hongshu Sui
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Shang Zhao
- Department of Pathophysiology, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Xingmei Gao
- Department of Neurology, People's Hospital of Binzhou, Binzhou, China
| | - Yanping Su
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, China
| | - Peng Qu
- Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
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17
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Peng Y, Tang D, Zhao M, Kajiyama H, Kikkawa F, Kondo Y. Long non-coding RNA: A recently accentuated molecule in chemoresistance in cancer. Cancer Metastasis Rev 2021; 39:825-835. [PMID: 32594276 DOI: 10.1007/s10555-020-09910-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemotherapy is one of the important and effective options for cancer treatment in the past decades. Although the response rate of initial chemotherapy is considerably high in certain types of cancers, such as ovarian cancer and lung cancer, the patients frequently suffer from chemoresistance and recurrence of disease. Recent genome-wide studies have shown that the large number of long non-coding RNAs (lncRNAs) are transcribed from the human genome and involved in many biological processes including carcinogenesis. They aberrantly regulate variety of cell functions, such as cell cycle, apoptosis, autophagy, and metabolisms, which are associated with chemosensitivity. Therefore, understanding the biological and clinical impacts of lncRNAs on tumor behavior and its potential as a predictive biomarker for chemotherapy effectiveness is highly desired. In this review, we classify the major mechanisms of lncRNA-related chemoresistance and provide theoretical evidences for targeting lncRNAs in certain types of cancers that may open up new therapeutic paradigm for cancer treatment.
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Affiliation(s)
- Yang Peng
- Fourth Department of Gynecologic Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410000, Hunan, China.,Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan.,Division of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Dihong Tang
- Fourth Department of Gynecologic Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410000, Hunan, China
| | - Meng Zhao
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Hiroaki Kajiyama
- Division of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Fumitaka Kikkawa
- Division of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan.
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18
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Thakuri BKC, Zhang J, Zhao J, Nguyen LN, Nguyen LNT, Schank M, Khanal S, Dang X, Cao D, Lu Z, Wu XY, Jiang Y, El Gazzar M, Ning S, Wang L, Moorman JP, Yao ZQ. HCV-Associated Exosomes Upregulate RUNXOR and RUNX1 Expressions to Promote MDSC Expansion and Suppressive Functions through STAT3-miR124 Axis. Cells 2020; 9:cells9122715. [PMID: 33353065 PMCID: PMC7766103 DOI: 10.3390/cells9122715] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
RUNX1 overlapping RNA (RUNXOR) is a long non-coding RNA and plays a pivotal role in the differentiation of myeloid cells via targeting runt-related transcription factor 1 (RUNX1). We and others have previously reported that myeloid-derived suppressor cells (MDSCs) expand and inhibit host immune responses during chronic viral infections; however, the mechanisms responsible for MDSC differentiation and suppressive functions, in particular the role of RUNXOR–RUNX1, remain unclear. Here, we demonstrated that RUNXOR and RUNX1 expressions are significantly upregulated and associated with elevated levels of immunosuppressive molecules, such as arginase 1 (Arg1), inducible nitric oxide synthase (iNOS), signal transducer and activator of transcription 3 (STAT3), and reactive oxygen species (ROS) in MDSCs during chronic hepatitis C virus (HCV) infection. Mechanistically, we discovered that HCV-associated exosomes (HCV-Exo) can induce the expressions of RUNXOR and RUNX1, which in turn regulates miR-124 expression via STAT3 signaling, thereby promoting MDSC differentiation and suppressive functions. Importantly, overexpression of RUNXOR in healthy CD33+ myeloid cells promoted differentiation and suppressive functions of MDSCs. Conversely, silencing RUNXOR or RUNX1 expression in HCV-derived CD33+ myeloid cells significantly inhibited their differentiation and expressions of suppressive molecules and improved the function of co-cultured autologous CD4 T cells. Taken together, these results indicate that the RUNXOR–RUNX1–STAT3–miR124 axis enhances the differentiation and suppressive functions of MDSCs and could be a potential target for immunomodulation in conjunction with antiviral therapy during chronic HCV infection.
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Affiliation(s)
- Bal Krishna Chand Thakuri
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Juan Zhao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Lam N. Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Lam N. T. Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Madison Schank
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Sushant Khanal
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Xindi Dang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Dechao Cao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Zeyuan Lu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Xiao Y. Wu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Yong Jiang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
| | - Mohamed El Gazzar
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
| | - Shunbin Ning
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Ling Wang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Jonathan P. Moorman
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
| | - Zhi Q. Yao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
- Correspondence: ; Tel.: +1-423-439-8029; Fax: +1-423-439-7010
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19
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Abstract
Long noncoding RNAs (lncRNAs) have recently been discovered and are increasingly recognized as vital components of modern molecular biology. Accumulating evidence shows that lncRNAs have emerged as important mediators in diverse biological processes such as cell differentiation, pluripotency, and tumorigenesis, while the function of lncRNAs in the field of normal and malignant hematopoiesis remains to be further elucidated. Here, we widely reviewed recent advances and summarize the characteristics and basic mechanisms of lncRNAs and keep abreast of developments of lncRNAs within the field of normal and malignant hematopoiesis. Based on gene regulatory networks at different levels of lncRNAs participation, lncRNAs have been shown to regulate gene expression from epigenetics, transcription and post transcription. The expression of lncRNAs is highly cell-specific and critical for the development and activation of hematopoiesis. Moreover, we also summarized the role of lncRNAs involved in hematological malignancies in recent years. LncRNAs have been found to play an emerging role in normal and malignant hematopoiesis, which may provide novel ideas for the diagnosis and therapeutic targets of hematological diseases in the foreseeable future.
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20
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Aznaourova M, Schmerer N, Schmeck B, Schulte LN. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci. Front Genet 2020; 11:527484. [PMID: 33329688 PMCID: PMC7735109 DOI: 10.3389/fgene.2020.527484] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.
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Affiliation(s)
- Marina Aznaourova
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Nils Schmerer
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
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21
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Shabgah AG, Salmaninejad A, Thangavelu L, Alexander M, Yumashev AV, Goleij P, Hedayati-Moghadam M, Mohammadi H, Ahmadi M, Navashenaq JG. The role of non-coding genome in the behavior of infiltrated myeloid-derived suppressor cells in tumor microenvironment; a perspective and state-of-the-art in cancer targeted therapy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 161:17-26. [PMID: 33259833 DOI: 10.1016/j.pbiomolbio.2020.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022]
Abstract
Cancer is one of the healthcare problems that affect many communities around the world. Many factors contribute to cancer development. Besides, these factors are counted as the main impediment in cancer immunotherapy. Myeloid-derived suppressor cells (MDSCs) are one of these impediments. MDSCs inhibit the immune responses through various mechanisms such as inhibitory cytokine release and nitric oxide metabolite production. Several factors are involved in forming these cells, including tumor secreted cytokine and chemokines, transcription factors, and non-coding RNA. In the meantime, micro-RNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the vital gene regulatory elements that affect gene expression. In this study, we are going to discuss the role of miRNAs and lncRNAs in MDSCs development in a cancer situation. It is hoped that miRNA and lncRNAs targeting may prevent the growth and development of these inhibitory cells in the cancer environment.
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Affiliation(s)
- Arezoo Gowhari Shabgah
- School of Medicine, Bam University of Medical Sciences, Bam, Iran; Student Research Committee, Bam University of Medical Sciences, Bam, Iran
| | - Arash Salmaninejad
- Department of Medical Genetics, Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Lakshmi Thangavelu
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | | | - Alexei Valerievich Yumashev
- Department of Prosthetic Dentistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Pouya Goleij
- Sana Institute of Higher Education, Faculty of Biology, Department of Genetics, Sari, Iran
| | | | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran; Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Majid Ahmadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jamshid Gholizadeh Navashenaq
- Student Research Committee, Bam University of Medical Sciences, Bam, Iran; Noncommunicable Diseases Research Center, Bam University of Medical Sciences, Bam, Iran.
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22
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Gurnari C, Pagliuca S, Visconte V. Deciphering the Therapeutic Resistance in Acute Myeloid Leukemia. Int J Mol Sci 2020; 21:ijms21228505. [PMID: 33198085 PMCID: PMC7697160 DOI: 10.3390/ijms21228505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is a clonal hematopoietic disorder characterized by abnormal proliferation, lack of cellular differentiation, and infiltration of bone marrow, peripheral blood, or other organs. Induction failure and in general resistance to chemotherapeutic agents represent a hindrance for improving survival outcomes in AML. Here, we review the latest insights in AML biology concerning refractoriness to therapies with a specific focus on cytarabine and daunorubicin which still represent milestones agents for inducing therapeutic response and disease eradication. However, failure to achieve complete remission in AML is still high especially in elderly patients (40-60% in patients >65 years old). Several lines of basic and clinical research have been employed to improve the achievement of complete remission. These lines of research include molecular targeted therapy and more recently immunotherapy. In terms of molecular targeted therapies, specific attention is given to DNMT3A and TP53 mutant AML by reviewing the mechanisms underlying epigenetic therapies' (e.g., hypomethylating agents) resistance and providing critical points and hints for possible future therapies overcoming AML refractoriness.
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Affiliation(s)
- Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Simona Pagliuca
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (C.G.); (S.P.)
- Correspondence: ; Tel.: +1-216-445-6895
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23
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Wang WJ, Li LY, Cui JW. Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis. Epigenetics Chromatin 2020; 13:49. [PMID: 33168103 PMCID: PMC7654176 DOI: 10.1186/s13072-020-00371-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
With the rapid development of next-generation sequencing technology, chromosome structural variation has gradually gained increased clinical significance in tumorigenesis. However, the molecular mechanism(s) underlying this structural variation remain poorly understood. A search of the literature shows that a three-dimensional chromatin state plays a vital role in inducing structural variation and in the gene expression profiles in tumorigenesis. Structural variants may result in changes in copy number or deletions of coding sequences, as well as the perturbation of structural chromatin features, especially topological domains, and disruption of interactions between genes and their regulatory elements. This review focuses recent work aiming at elucidating how structural variations develop and misregulate oncogenes and tumor suppressors, to provide general insights into tumor formation mechanisms and to provide potential targets for future anticancer therapies.
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Affiliation(s)
- Wen-Jun Wang
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
| | - Ling-Yu Li
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
| | - Jiu-Wei Cui
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
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24
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Safarzadeh E, Asadzadeh Z, Safaei S, Hatefi A, Derakhshani A, Giovannelli F, Brunetti O, Silvestris N, Baradaran B. MicroRNAs and lncRNAs-A New Layer of Myeloid-Derived Suppressor Cells Regulation. Front Immunol 2020; 11:572323. [PMID: 33133086 PMCID: PMC7562789 DOI: 10.3389/fimmu.2020.572323] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/28/2020] [Indexed: 12/23/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) constitute an important component in regulating immune responses in several abnormal physiological conditions such as cancer. Recently, novel regulatory tumor MDSC biology modulating mechanisms, including differentiation, expansion and function, were defined. There is growing evidence that miRNAs and long non-coding RNAs (lncRNA) are involved in modulating transcriptional factors to become complex regulatory networks that regulate the MDSCs in the tumor microenvironment. It is possible that aberrant expression of miRNAs and lncRNA contributes to MDSC biological characteristics under pathophysiological conditions. This review provides an overview on miRNAs and lncRNAs epiregulation of MDSCs development and immunosuppressive functions in cancer.
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Affiliation(s)
- Elham Safarzadeh
- Department of Microbiology & Immunology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Asadzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sahar Safaei
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arash Hatefi
- Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Afshin Derakhshani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Francesco Giovannelli
- Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Oronzo Brunetti
- Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Nicola Silvestris
- Medical Oncology Unit-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy.,Department of Biomedical Sciences and Human Oncology, Department of Internal Medicine and Oncology (DIMO)-University of Bari, Bari, Italy
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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25
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Guo C, Gao YY, Ju QQ, Zhang CX, Gong M, Li ZL. LINC00649 underexpression is an adverse prognostic marker in acute myeloid leukemia. BMC Cancer 2020; 20:841. [PMID: 32883226 PMCID: PMC7469387 DOI: 10.1186/s12885-020-07331-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/24/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNA) play a role in leukemogenesis, maintenance, development, and therapeutic resistance of AML. While few studies have focused on the prognostic significance of LINC00649 in AML, which we aim to investigate in this present study. METHODS We compared the expression level of LINC00649 between AML patients and healthy controls. The Kaplan-Meier curves of AML patients expressing high versus low level of LINC00649 was performed. The LINC00649 correlated genes/miRNAs/lncRNAs and methylation CpG sites were screened by Pearson correlation analysis with R (version 3.6.0), using TCGA-LAML database. The LINC00649 associated ceRNA network was established using lncBase 2.0 and miRWalk 2.0 online tools, combining results from correlation analysis. Finally, a prediction model was constructed using LASSO-Cox regression. RESULTS LINC00649 was underexpressed in bone marrow of AML group than that in healthy control group. The patients of LINC00649-low group have significantly inferior PFS and OS. A total of 154 mRNAs, 31 miRNAs, 28 lncRNAs and 1590 methylated CpG sites were identified to be significantly correlated with LINC00649. Furthermore, the network of ceRNA was established with 6 miRNAs and 122 mRNAs. The Lasso-Cox model fitted OS/PFS to novel prediction models, which integrated clinical factors, ELN risk stratification, mRNA/miRNA expression and methylation profiles. The analysis of time-dependent ROC for our model showed a superior AUC (AUC = 0.916 at 1 year, AUC = 0.916 at 3 years, and AUC = 0.891 at 5 years). CONCLUSIONS Low expression of LINC00649 is a potential unfavorable prognostic marker for AML patients, which requires the further validation. The analysis by LASSO-COX regression identified a novel comprehensive model with a superior diagnostic utility, which integrated clinical and genetic variables.
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Affiliation(s)
- Chao Guo
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, China
| | - Ya-Yue Gao
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, China
| | - Qian-Qian Ju
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, China
| | - Chun-Xia Zhang
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, China
| | - Ming Gong
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, China
| | - Zhen-Ling Li
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, China.
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26
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Liu Y, Sun P, Zhao Y, Liu B. The role of long non-coding RNAs and downstream signaling pathways in leukemia progression. Hematol Oncol 2020; 39:27-40. [PMID: 32621547 DOI: 10.1002/hon.2776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 01/17/2023]
Abstract
The study of long non-coding RNAs (lncRNA) is a newly established field and our knowledge about them is rapidly growing. These kinds of RNAs are unchanged parts of the genome throughout evolution, that modulate cell growth, differentiation, and apoptosis during diverse physiological and pathological processes including leukemia development. They have the capability to be useful biomarkers for the diagnosis, clinical typing, prognosis, as well as potential therapeutic targets. In this study, we summarized the role of lncRNAs in the expression and function of white blood cells and oncogenic transformation into four main types of leukemia.
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Affiliation(s)
- Yadong Liu
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, China
| | - Penghao Sun
- Department of Andrology, The First Hospital of Jilin University, Changchun, China
| | - Yuhao Zhao
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Bin Liu
- Department of Hand Surgery, The First Hospital of Jilin University, Changchun, China
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27
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Han C, Sun LY, Wang WT, Sun YM, Chen YQ. Non-coding RNAs in cancers with chromosomal rearrangements: the signatures, causes, functions and implications. J Mol Cell Biol 2020; 11:886-898. [PMID: 31361891 PMCID: PMC6884712 DOI: 10.1093/jmcb/mjz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/24/2019] [Accepted: 05/26/2019] [Indexed: 12/25/2022] Open
Abstract
Chromosomal translocation leads to the juxtaposition of two otherwise separate DNA loci, which could result in gene fusion. These rearrangements at the DNA level are catastrophic events and often have causal roles in tumorigenesis. The oncogenic DNA messages are transferred to RNA molecules, which are in most cases translated into cancerous fusion proteins. Gene expression programs and signaling pathways are altered in these cytogenetically abnormal contexts. Notably, non-coding RNAs have attracted increasing attention and are believed to be tightly associated with chromosome-rearranged cancers. These RNAs not only function as modulators in downstream pathways but also directly affect chromosomal translocation or the associated products. This review summarizes recent research advances on the relationship between non-coding RNAs and chromosomal translocations and on diverse functions of non-coding RNAs in cancers with chromosomal rearrangements.
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Affiliation(s)
- Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lin-Yu Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Zhu Y, Yan Z, Tang Z, Li W. Novel Approaches to Profile Functional Long Noncoding RNAs Associated with Stem Cell Pluripotency. Curr Genomics 2020; 21:37-45. [PMID: 32655297 PMCID: PMC7324891 DOI: 10.2174/1389202921666200210142840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/17/2020] [Accepted: 01/31/2020] [Indexed: 12/11/2022] Open
Abstract
The pluripotent state of stem cells depends on the complicated network orchestrated by thousands of factors and genes. Long noncoding RNAs (lncRNAs) are a class of RNA longer than 200 nt without a protein-coding function. Single-cell sequencing studies have identified hundreds of lncRNAs with dynamic changes in somatic cell reprogramming. Accumulating evidence suggests that they participate in the initiation of reprogramming, maintenance of pluripotency, and developmental processes by cis and/or trans mechanisms. In particular, they may interact with proteins, RNAs, and chromatin modifier complexes to form an intricate pluripotency-associated network. In this review, we focus on recent progress in approaches to profiling functional lncRNAs in somatic cell reprogramming and cell differentiation.
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Affiliation(s)
- Yanbo Zhu
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Zi Yan
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Ze Tang
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
| | - Wei Li
- 1Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin130021, China; 2Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin130021, China; 3Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin130021, China
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29
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Jia L, Wang Y, Wang C, Du Z, Zhang S, Wen X, Zhou L, Li H, Chen H, Li D, Zhang S, Li W, Xu W, Hoffman AR, Cui J, Hu JF. Oplr16 serves as a novel chromatin factor to control stem cell fate by modulating pluripotency-specific chromosomal looping and TET2-mediated DNA demethylation. Nucleic Acids Res 2020; 48:3935-3948. [PMID: 32055844 PMCID: PMC7144914 DOI: 10.1093/nar/gkaa097] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/03/2023] Open
Abstract
Formation of a pluripotency-specific chromatin network is a critical event in reprogramming somatic cells into pluripotent status. To characterize the regulatory components in this process, we used ‘chromatin RNA in situ reverse transcription sequencing’ (CRIST-seq) to profile RNA components that interact with the pluripotency master gene Oct4. Using this approach, we identified a novel nuclear lncRNA Oplr16 that was closely involved in the initiation of reprogramming. Oplr16 not only interacted with the Oct4 promoter and regulated its activity, but it was also specifically activated during reprogramming to pluripotency. Active expression of Oplr16 was required for optimal maintenance of pluripotency in embryonic stem cells. Oplr16 was also able to enhance reprogramming of fibroblasts into pluripotent cells. RNA reverse transcription-associated trap sequencing (RAT-seq) indicated that Oplr16 interacted with multiple target genes related to stem cell self-renewal. Of note, Oplr16 utilized its 3′-fragment to recruit the chromatin factor SMC1 to orchestrate pluripotency-specific intrachromosomal looping. After binding to the Oct4 promoter, Oplr16 recruited TET2 to induce DNA demethylation and activate Oct4 in fibroblasts, leading to enhanced reprogramming. These data suggest that Oplr16 may act as a pivotal chromatin factor to control stem cell fate by modulating chromatin architecture and DNA demethylation.
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Affiliation(s)
- Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Hui Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.,Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
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30
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Gao J, Wang F, Wu P, Chen Y, Jia Y. Aberrant LncRNA Expression in Leukemia. J Cancer 2020; 11:4284-4296. [PMID: 32368311 PMCID: PMC7196264 DOI: 10.7150/jca.42093] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Leukemia is a common malignant cancer of the hematopoietic system, whose pathogenesis has not been fully elucidated. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides without protein-coding function. Recent studies report their role in cellular processes such as the regulation of gene expression, as well as in the carcinogenesis, occurrence, development, and prognosis of various tumors. Evidence indicating relationships between a variety of lncRNAs and leukemia pathophysiology has increased dramatically in the previous decade, with specific lncRNAs expected to serve as diagnostic biomarkers, novel therapeutic targets, and predictors of clinical outcomes. Furthermore, these lncRNAs might offer insight into disease pathogenesis and novel treatment options. This review summarizes progress in studies on the role(s) of lncRNAs in leukemia.
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Affiliation(s)
- Jie Gao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fujue Wang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Pengqiang Wu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yingying Chen
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yongqian Jia
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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31
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Zhu Y, Yan Z, Du Z, Zhang S, Fu C, Meng Y, Wen X, Wang Y, Hoffman AR, Hu JF, Cui J, Li W. Osblr8 orchestrates intrachromosomal loop structure required for maintaining stem cell pluripotency. Int J Biol Sci 2020; 16:1861-1875. [PMID: 32398955 PMCID: PMC7211171 DOI: 10.7150/ijbs.45112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/22/2020] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs), derived from reprogramming of somatic cells by a cocktail of transcription factors, have the capacity for unlimited self-renewal and the ability to differentiate into all of cell types present in the body. iPSCs may have therapeutic potential in regenerative medicine, replacing injured tissues or even whole organs. In this study, we examine epigenetic factors embedded in the specific 3-dimensional intrachromosomal architecture required for the activation of endogenous pluripotency genes. Using chromatin RNA in situ reverse transcription sequencing (CRIST-seq), we identified an Oct4-Sox2 binding long noncoding RNA, referred as to Osblr8, that is present in association with pluripotency status. Osblr8 was highly expressed in iPSCs and E14 embryonic stem cells, but it was silenced in fibroblasts. By using shRNA to knock down Osblr8, we found that this lncRNA was required for the maintenance of pluripotency. Overexpression of Osblr8 activated endogenous stem cell core factor genes. Mechanistically, Osblr8 participated in the formation of an intrachromosomal looping structure that is required to activate stem cell core factors during reprogramming. In summary, we have demonstrated that lncRNA Osblr8 is a chromatin architecture modulator of pluripotency-associated master gene promoters, highlighting its critical epigenetic role in reprogramming.
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Affiliation(s)
- Yanbo Zhu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zi Yan
- Division of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Changhao Fu
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ying Meng
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Yizhuo Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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32
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Association of long non-coding RNA and leukemia: A systematic review. Gene 2020; 735:144405. [DOI: 10.1016/j.gene.2020.144405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/27/2020] [Indexed: 12/12/2022]
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33
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Xiong X, Feng Y, Li L, Yao J, Zhou M, Zhao P, Huang F, Zeng L, Yuan L. Long non‑coding RNA SNHG1 promotes breast cancer progression by regulation of LMO4. Oncol Rep 2020; 43:1503-1515. [PMID: 32323846 PMCID: PMC7107776 DOI: 10.3892/or.2020.7530] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) was reported to be a critical regulator of tumorigenesis and is frequently deregulated in several cancer types. However, the exact mechanism by which SNHG1 contributes to breast cancer progression has not been fully elucidated. The identification of the molecular mechanism of SNHG1 is important for understanding the development of breast cancer and for improving the prognosis of the patients with this disease. In the present study, increased expression levels of SNHG1 were noted in breast cancer tumors following analysis of differentially expressed lncRNAs between 1,063 tumor and 102 normal tissues derived from The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) dataset. This finding was further validated using 50 pairs of normal and tumor tissues that were collected from patients with breast cancer. Notably, SNHG1 expression was significantly correlated with estrogen receptor (ER)/progesterone receptor (PR) negative status (ER−/PR−) and advanced clinical stage in breast cancer tissues. Knockdown of SNHG1 led to cell growth arrest, cell cycle redistribution and cell migration inhibition of breast cancer cells. The miRDB database predicted that miR-573 interacts with SNHG1. RT-PCR confirmed the negative regulation of miR-573 levels by SNHG1 in breast cancer cells and the Dual-luciferase reporter assay confirmed their complementary binding. The repression of miR-573 by SNGH1 decreased LIM domain only 4 (LMO4) mRNA and protein expression levels in the breast cancer cell lines tested and induced the expression of cyclin D1 and cyclin E. In vitro experiments indicated that LMO4 overexpression could reverse siSNHG1-induced cell growth arrest, cell cycle redistribution and inhibition of cell migration in breast cancer cells. Moreover, the tumor xenograft model indicated that SNHG1 knockdown inhibited MDA-MB-231 growth in vivo and LMO4 overexpression reversed the tumor growth inhibition induced by SNHG1 knockdown. The present study demonstrated that SNHG1 acts as a novel oncogene in breast cancer via the SNHG/miR-573/LMO4 axis and that it could be a promising therapeutic target for patients with breast cancer.
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Affiliation(s)
- Xiang Xiong
- Department of Burn and Plastic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yeqian Feng
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Lun Li
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Jia Yao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Meirong Zhou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Piao Zhao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Feilong Huang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Liyun Zeng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Liqin Yuan
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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34
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Wang C, Jia L, Wang Y, Du Z, Zhou L, Wen X, Li H, Zhang S, Chen H, Chen N, Chen J, Zhu Y, Nie Y, Celic I, Gao S, Zhang S, Hoffman AR, Li W, Hu JF, Cui J. Genome-wide interaction target profiling reveals a novel Peblr20-eRNA activation pathway to control stem cell pluripotency. Am J Cancer Res 2020; 10:353-370. [PMID: 31903125 PMCID: PMC6929617 DOI: 10.7150/thno.39093] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/14/2019] [Indexed: 12/19/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs) constitute an important component of the regulatory apparatus that controls stem cell pluripotency. However, the specific mechanisms utilized by these lncRNAs in the control of pluripotency are not fully characterized. Methods: We utilized a RNA reverse transcription-associated trap sequencing (RAT-seq) approach to profile the mouse genome-wide interaction targets for lncRNAs that are screened by RNA-seq. Results: We identified Peblr20 (Pou5F1 enhancer binding lncRNA 20) as a novel lncRNA that is associated with stem cell reprogramming. Peblr20 was differentially transcribed in fibroblasts compared to induced pluripotent stem cells (iPSCs). Notably, we found that Peblr20 utilized a trans mechanism to interact with the regulatory elements of multiple stemness genes. Using gain- and loss-of-function experiments, we showed that knockdown of Peblr20 caused iPSCs to exit from pluripotency, while overexpression of Peblr20 activated endogenous Pou5F1 expression. We further showed that Peblr20 promoted pluripotent reprogramming. Mechanistically, we demonstrated that Peblr20 activated endogenous Pou5F1 by binding to the Pou5F1 enhancer in trans, recruiting TET2 demethylase and activating the enhancer-transcribed RNAs. Conclusions: Our data reveal a novel epigenetic mechanism by which a lncRNA controls the fate of stem cells by trans-regulating the Pou5F1 enhancer RNA pathway. We demonstrate the potential for leveraging lncRNA biology to enhance the generation of stem cells for regenerative medicine.
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Abstract
Comprehensive cataloguing of the acute myeloid leukaemia (AML) genome has revealed a high frequency of mutations and deletions in epigenetic factors that are frequently linked to treatment resistance and poor patient outcome. In this review, we discuss how the epigenetic mechanisms that underpin normal haematopoiesis are subverted in AML, and in particular how these processes are altered in childhood and adolescent leukaemias. We also provide a brief summary of the burgeoning field of epigenetic-based therapies, and how AML treatment might be improved through provision of better conceptual frameworks for understanding the pleiotropic molecular effects of epigenetic disruption.
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Affiliation(s)
- Luke Jones
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Peter McCarthy
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
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36
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Gourvest M, Brousset P, Bousquet M. Long Noncoding RNAs in Acute Myeloid Leukemia: Functional Characterization and Clinical Relevance. Cancers (Basel) 2019; 11:cancers11111638. [PMID: 31653018 PMCID: PMC6896193 DOI: 10.3390/cancers11111638] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022] Open
Abstract
Acute Myeloid Leukemia (AML) is the most common form of leukemia in adults with an incidence of 4.3 per 100,000 cases per year. Historically, the identification of genetic alterations in AML focused on protein-coding genes to provide biomarkers and to understand the molecular complexity of AML. Despite these findings and because of the heterogeneity of this disease, questions as to the molecular mechanisms underlying AML development and progression remained unsolved. Recently, transcriptome-wide profiling approaches have uncovered a large family of long noncoding RNAs (lncRNAs). Larger than 200 nucleotides and with no apparent protein coding potential, lncRNAs could unveil a new set of players in AML development. Originally considered as dark matter, lncRNAs have critical roles to play in the different steps of gene expression and thus affect cellular homeostasis including proliferation, survival, differentiation, migration or genomic stability. Consequently, lncRNAs are found to be differentially expressed in tumors, notably in AML, and linked to the transformation of healthy cells into leukemic cells. In this review, we aim to summarize the knowledge concerning lncRNAs functions and implications in AML, with a particular emphasis on their prognostic and therapeutic potential.
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Affiliation(s)
- Morgane Gourvest
- Cancer Research Center of Toulouse (CRCT), UMR1037 INSERM-Université Paul Sabatier Toulouse III-CNRS ERL5294, 31037 Toulouse, France.
| | - Pierre Brousset
- Cancer Research Center of Toulouse (CRCT), UMR1037 INSERM-Université Paul Sabatier Toulouse III-CNRS ERL5294, 31037 Toulouse, France.
| | - Marina Bousquet
- Cancer Research Center of Toulouse (CRCT), UMR1037 INSERM-Université Paul Sabatier Toulouse III-CNRS ERL5294, 31037 Toulouse, France.
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37
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Thoms JAI, Beck D, Pimanda JE. Transcriptional networks in acute myeloid leukemia. Genes Chromosomes Cancer 2019; 58:859-874. [PMID: 31369171 DOI: 10.1002/gcc.22794] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease characterized by a diverse range of recurrent molecular aberrations that occur in many different combinations. Components of transcriptional networks are a common target of these aberrations, leading to network-wide changes and deployment of novel or developmentally inappropriate transcriptional programs. Genome-wide techniques are beginning to reveal the full complexity of normal hematopoietic stem cell transcriptional networks and the extent to which they are deregulated in AML, and new understandings of the mechanisms by which AML cells maintain self-renewal and block differentiation are starting to emerge. The hope is that increased understanding of the network architecture in AML will lead to identification of key oncogenic dependencies that are downstream of multiple network aberrations, and that this knowledge will be translated into new therapies that target these dependencies. Here, we review the current state of knowledge of network perturbation in AML with a focus on major mechanisms of transcription factor dysregulation, including mutation, translocation, and transcriptional dysregulation, and discuss how these perturbations propagate across transcriptional networks. We will also review emerging mechanisms of network disruption, and briefly discuss how increased knowledge of network disruption is already being used to develop new therapies.
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Affiliation(s)
- Julie A I Thoms
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Dominik Beck
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - John E Pimanda
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, New South Wales, Australia
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38
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Schnake N, Hinojosa M, Gutiérrez S. Identification of a novel long non-coding RNA within RUNX1 intron 5. Hum Genomics 2019; 13:33. [PMID: 31366376 PMCID: PMC6670153 DOI: 10.1186/s40246-019-0219-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/19/2019] [Indexed: 12/26/2022] Open
Abstract
Background RUNX1 gene, a master regulator of the hematopoietic process, participates in pathological conditions as a partner for several genes in chromosomal translocations. One of the most frequent chromosomal translocations found in acute myeloid leukemia patients is the t(8;21), in which RUNX1 and ETO genes recombine. In RUNX1 gene, the DNA double-strand breaks that originate the t(8;21) are generated in the intron 5, specifically within three regions designated as BCR1, BCR2, and BCR3. To date, what determines that these regions are more susceptible to DNA double-strand breaks is not completely clear. In this report, we characterized RUNX1 intron 5, by analyzing DNase-seq and ChIP-seq data, available in the ENCODE Project server, to evaluate DNaseI hypersensitivity and the presence of the epigenetic mark H3K4me3 in 124 and 51 cell types, respectively. Results Our results show that intron 5 exhibits an epigenetic mark distribution similar to known promoter regions. Moreover, using the online tool YAPP and available CAGE data from the ENCODE Project server, we identified several putative transcription start sites within intron 5 in regions BCR2 and BCR3. Finally, available EST data was analyzed, identifying a novel uncharacterized long non-coding RNA, which is expressed in hematopoietic cell lines as shown by RT-PCR. Our data suggests that the core promoter of the novel long non-coding RNA locates within the region BCR3. Conclusion We identified a novel long non-coding RNA within RUNX1 intron 5, transcribed from a promoter located in the region BCR3, one of the chromosomal breakpoints of RUNX1 gene. Electronic supplementary material The online version of this article (10.1186/s40246-019-0219-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolás Schnake
- Laboratory of Epigenetics [EpiGene], Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile
| | - Marcela Hinojosa
- Laboratory of Epigenetics [EpiGene], Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile
| | - Soraya Gutiérrez
- Laboratory of Epigenetics [EpiGene], Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile.
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39
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Leija Montoya G, González Ramírez J, Sandoval Basilio J, Serafín Higuera I, Isiordia Espinoza M, González González R, Serafín Higuera N. Long Non-coding RNAs: Regulators of the Activity of Myeloid-Derived Suppressor Cells. Front Immunol 2019; 10:1734. [PMID: 31404149 PMCID: PMC6671873 DOI: 10.3389/fimmu.2019.01734] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/09/2019] [Indexed: 12/29/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous cell population with potent immunosuppressive functions. They play major roles in cancer and many of the pathologic conditions associated with inflammation. Long non-coding RNAs (lncRNAs) are untranslated functional RNA molecules. The lncRNAs are involved in the control of a wide variety of cellular processes and are dysregulated in different diseases. They can participate in the modulation of immune function and activity of inflammatory cells, including MDSCs. This mini review focuses on the emerging role of lncRNAs in MDSC activity. We summarize how lncRNAs modulate the generation, recruitment, and immunosuppressive functions of MDSCs and the underlying mechanisms.
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Affiliation(s)
| | | | | | | | - Mario Isiordia Espinoza
- División de Ciencias Biomédicas, Departamento de Clínicas, Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos, Guadalajara, Mexico
| | | | - Nicolás Serafín Higuera
- Unidad de Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California, Mexicali, Mexico
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40
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Zhang S, Wang Y, Jia L, Wen X, Du Z, Wang C, Hao Y, Yu D, Zhou L, Chen N, Chen J, Chen H, Zhang H, Celik I, Gülsoy G, Luo J, Qin B, Cui X, Liu Z, Zhang S, Esteban MA, Ay F, Xu W, Chen R, Li W, Hoffman AR, Hu JF, Cui J. Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing. Genome Res 2019; 29:1521-1532. [PMID: 31315906 PMCID: PMC6724666 DOI: 10.1101/gr.244996.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/10/2019] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a “chromatin-RNA in situ reverse transcription sequencing” (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements by combining the simplicity of RNA biotin labeling with the specificity of the CRISPR/Cas9 system. Using gene-specific gRNAs, we describe a pluripotency-specific lncRNA interacting network in the promoters of Sox2 and Pou5f1, two critical stem cell factors that are required for the maintenance of pluripotency. The promoter-interacting lncRNAs were specifically activated during reprogramming into pluripotency. Knockdown of these lncRNAs caused the stem cells to exit from pluripotency. In contrast, overexpression of the pluripotency-associated lncRNA activated the promoters of core stem cell factor genes and enhanced fibroblast reprogramming into pluripotency. These CRIST-seq data suggest that the Sox2 and Pou5f1 promoters are organized within a unique lncRNA interaction network that determines the fate of pluripotency during reprogramming. This CRIST approach may be broadly used to map lncRNA interaction networks at target loci across the genome.
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Affiliation(s)
- Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Yajing Hao
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Dehai Yu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Naifei Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Jingcheng Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Huiling Chen
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hui Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China
| | - Ilkay Celik
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Günhan Gülsoy
- Google Incorporated, Mountain View, California 94043, USA
| | - Jianjun Luo
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Baoming Qin
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China
| | - Xueling Cui
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Zhonghui Liu
- Department of Immunology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Miguel A Esteban
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, P.R. China
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Runsheng Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130061, P.R. China
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41
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Ng M, Heckl D, Klusmann JH. The Regulatory Roles of Long Noncoding RNAs in Acute Myeloid Leukemia. Front Oncol 2019; 9:570. [PMID: 31338324 PMCID: PMC6629768 DOI: 10.3389/fonc.2019.00570] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/12/2019] [Indexed: 01/23/2023] Open
Abstract
In this post-genomic era, long noncoding RNAs (lncRNAs) are rapidly gaining recognition for their crucial roles across diverse biological processes and contexts. The human blood system is no exception, where dozens of lncRNAs have been established as regulators of normal and/or malignant hematopoiesis, and where ongoing works continue to uncover novel lncRNA functions. Our review focuses on lncRNAs that are involved in the pathogenesis of acute myeloid leukemia (AML) and the mechanisms through which they control gene expression in this disease context. We also comment on genome-wide sequencing or profiling studies that have implicated large sets of lncRNAs in AML pathophysiology.
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Affiliation(s)
- Michelle Ng
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dirk Heckl
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jan-Henning Klusmann
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
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42
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Dornelles-Wawruk H, Soledad Heredia R, de Paula-Junior MR, Cardoso MTO, Bonadio RS, Dos Reis BF, Pic-Taylor A, de Oliveira SF, Mazzeu JF. A Balanced Reciprocal Translocation t(2;9)(p25;q13) Disrupting the LINC00299 Gene in a Patient with Intellectual Disability. Mol Syndromol 2019; 10:234-238. [PMID: 31602198 DOI: 10.1159/000500397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a class of noncoding RNAs implicated in several biological processes. LincRNA 299 (LINC00299) maps to 2p25.1 and its function is still unknown. However, this gene has been proposed as a candidate for intellectual disability (ID) in a patient with a balanced translocation where the breakpoint disrupted its ORF. Here, we describe a new case of LINC00299 disruption associated with ID. The individual, a 42-year-old woman, was referred to the clinical geneticist because of her son who had severe syndromic ID. G-banding and chromosomal microarray analysis were performed. Karyotyping of the boy revealed an extranumerary derivative chromosome identified as an unbalanced translocation between chromosomes 2 and 9 of maternal origin. The mother's karyotype showed a balanced translocation 46,XX,t(2;9)(p25;q13). Chromosomal microarray indicated a disruption of LINC00299. These data corroborate the role of LINC00299 as a causative gene for ID and broadens the spectrum of LINC00299-related phenotypes.
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Affiliation(s)
| | - Romina Soledad Heredia
- Hospital de Apoio de Brasília, Secretaria de Estado de Saúde do Distrito Federal, Brasilia, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasilia, Brazil
| | | | | | - Raphael S Bonadio
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Bianca F Dos Reis
- Hospital de Apoio de Brasília, Secretaria de Estado de Saúde do Distrito Federal, Brasilia, Brazil
| | - Aline Pic-Taylor
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Silviene F de Oliveira
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, Brazil
| | - Juliana F Mazzeu
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasilia, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasilia, Brazil.,Faculdade de Medicina, Universidade de Brasília, Brasilia, Brazil
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43
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Liu Y, Cheng Z, Pang Y, Cui L, Qian T, Quan L, Zhao H, Shi J, Ke X, Fu L. Role of microRNAs, circRNAs and long noncoding RNAs in acute myeloid leukemia. J Hematol Oncol 2019; 12:51. [PMID: 31126316 PMCID: PMC6534901 DOI: 10.1186/s13045-019-0734-5] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/16/2019] [Indexed: 12/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a malignant tumor of the immature myeloid hematopoietic cells in the bone marrow (BM). It is a highly heterogeneous disease, with rising morbidity and mortality in older patients. Although researches over the past decades have improved our understanding of AML, its pathogenesis has not yet been fully elucidated. Long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) are three noncoding RNA (ncRNA) molecules that regulate DNA transcription and translation. With the development of RNA-Seq technology, more and more ncRNAs that are closely related to AML leukemogenesis have been discovered. Numerous studies have found that these ncRNAs play an important role in leukemia cell proliferation, differentiation, and apoptosis. Some may potentially be used as prognostic biomarkers. In this systematic review, we briefly described the characteristics and molecular functions of three groups of ncRNAs, including lncRNAs, miRNAs, and circRNAs, and discussed their relationships with AML in detail.
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Affiliation(s)
- Yan Liu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Zhiheng Cheng
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yifan Pang
- Department of Medicine, William Beaumont Hospital, Royal Oak, MI, 48073, USA
| | - Longzhen Cui
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China
| | - Tingting Qian
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Liang Quan
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Hongyou Zhao
- Department of Laser Medicine, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jinlong Shi
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China. .,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China. .,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, 475000, China.
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44
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Lei L, Xia S, Liu D, Li X, Feng J, Zhu Y, Hu J, Xia L, Guo L, Chen F, Cheng H, Chen K, Hu H, Chen X, Li F, Zhong S, Mittal N, Yang G, Qian Z, Han L, He C. Genome-wide characterization of lncRNAs in acute myeloid leukemia. Brief Bioinform 2019; 19:627-635. [PMID: 28203711 DOI: 10.1093/bib/bbx007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a large family of noncoding RNAs that play a critical role in various normal bioprocesses as well as tumorigenesis. However, the expression patterns and biological functions of lncRNAs in acute leukemia have not been well studied. Here, we performed transcriptome-wide lncRNA expression profiling of acute myeloid leukemia (AML) patient samples, along with non-leukemia control hematopoietic samples. We found that lncRNAs were differentially expressed in AML samples relative to control samples. Notably, we identified that lncRNAs upregulated in AML (relative to the control samples) are associated with a lower degree of DNA methylation and a higher ratio of being bound by transcription factors such as SP1, STAT4, ATF-2 and ELK-1 compared with those downregulated in AML. Moreover, an enrichment of H3K4me3 and a depletion of H3K27me3 were observed in upregulated lncRNAs in AML. Expression patterns of three types of lncRNAs (antisense, enhancer and intergenic lncRNAs) have previously been characterized. Of the identified lncRNAs, we found that high expression level lncRNA LOC285758 is associated with the poor prognosis in AML patients. Furthermore, we found that LOC285758 regulates proliferation of AML cell lines by enhancing the expression of HDAC2, a key factor in carcinogenesis. Collectively, our study depicts a landscape of important lncRNAs in AML and provides novel potential therapeutic targets and prognostic markers for AML treatment.
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Affiliation(s)
- Lijun Lei
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Siyu Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Dan Liu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaoqing Li
- Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, China
| | - Jing Feng
- International School of Software, Wuhan University, Wuhan, China
| | - Yaqi Zhu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Hu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Linjian Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Lieping Guo
- Physician in Eastern Hepatobiliary Hospital, Hospital of Second Military Medical University, Wuhan, Hubei, China
| | - Fei Chen
- Zhongnan hospital of Wuhan University, Wuhan, China
| | - Hui Cheng
- Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ke Chen
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Hanyang Hu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaohua Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | | | - Shan Zhong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Nupur Mittal
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Guohua Yang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhijian Qian
- Department of Medicine and Cancer Research Center, University of Illinois at Chicago, Chicago, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
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45
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Long Non-Coding RNA and Acute Leukemia. Int J Mol Sci 2019; 20:ijms20030735. [PMID: 30744139 PMCID: PMC6387068 DOI: 10.3390/ijms20030735] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022] Open
Abstract
Acute leukemia (AL) is the main type of cancer in children worldwide. Mortality by this disease is high in developing countries and its etiology remains unanswered. Evidences showing the role of the long non-coding RNAs (lncRNAs) in the pathophysiology of hematological malignancies have increased drastically in the last decade. In addition to the contribution of these lncRNAs in leukemogenesis, recent studies have suggested that lncRNAs could be used as biomarkers in the diagnosis, prognosis, and therapeutic response in leukemia patients. The focus of this review is to describe the functional classification, biogenesis, and the role of lncRNAs in leukemogenesis, to summarize the evidence about the lncRNAs which are playing a role in AL, and how these genes could be useful as potential therapeutic targets.
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46
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Chen N, Zhao G, Yan X, Lv Z, Yin H, Zhang S, Song W, Li X, Li L, Du Z, Jia L, Zhou L, Li W, Hoffman AR, Hu JF, Cui J. A novel FLI1 exonic circular RNA promotes metastasis in breast cancer by coordinately regulating TET1 and DNMT1. Genome Biol 2018; 19:218. [PMID: 30537986 PMCID: PMC6290540 DOI: 10.1186/s13059-018-1594-y] [Citation(s) in RCA: 287] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/23/2018] [Indexed: 01/10/2023] Open
Abstract
Background Friend leukemia virus integration 1 (FLI1), an ETS transcription factor family member, acts as an oncogenic driver in hematological malignancies and promotes tumor growth in solid tumors. However, little is known about the mechanisms underlying the activation of this proto-oncogene in tumors. Results Immunohistochemical staining showed that FLI1 is aberrantly overexpressed in advanced stage and metastatic breast cancers. Using a CRISPR Cas9-guided immunoprecipitation assay, we identify a circular RNA in the FLI1 promoter chromatin complex, consisting of FLI1 exons 4-2-3, referred to as FECR1.Overexpression of FECR1 enhances invasiveness of MDA-MB231 breast cancer cells. Notably, FECR1 utilizes a positive feedback mechanism to activate FLI1 by inducing DNA hypomethylation in CpG islands of the promoter. FECR1 binds to the FLI1 promoter in cis and recruits TET1, a demethylase that is actively involved in DNA demethylation. FECR1 also binds to and downregulates in trans DNMT1, a methyltransferase that is essential for the maintenance of DNA methylation. Conclusions These data suggest that FECR1 circular RNA acts as an upstream regulator to control breast cancer tumor growth by coordinating the regulation of DNA methylating and demethylating enzymes. Thus, FLI1 drives tumor metastasis not only through the canonical oncoprotein pathway, but also by using epigenetic mechanisms mediated by its exonic circular RNA. Electronic supplementary material The online version of this article (10.1186/s13059-018-1594-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naifei Chen
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Gang Zhao
- Department of Breast Cancer Surgery, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Xu Yan
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Zheng Lv
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Hongmei Yin
- Department of General Internal Medicine, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Shilin Zhang
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Wei Song
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Xueli Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Lingyu Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Zhonghua Du
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Lin Jia
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Lei Zhou
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Wei Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China
| | - Andrew R Hoffman
- Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China. .,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA, 94304, USA.
| | - Jiuwei Cui
- Stem Cell and Cancer Center, The First Hospital of Jilin University, 71 Xinmin Street, Changchun, 133021, Jilin, China.
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47
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Du Z, Jia L, Wang Y, Wang C, Wen X, Chen J, Zhu Y, Yu D, Zhou L, Chen N, Zhang S, Celik I, Ay F, Gao S, Zhang S, Li W, Hoffman AR, Cui J, Hu JF. Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming. Sci Data 2018; 5:180255. [PMID: 30457566 PMCID: PMC6244186 DOI: 10.1038/sdata.2018.255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
Pluripotent stem cells hold great investigative potential for developmental biology and regenerative medicine. Recent studies suggest that long noncoding RNAs (lncRNAs) may function as key regulators of the maintenance and the lineage differentiation of stem cells. However, the underlying mechanisms by which lncRNAs affect the reprogramming process of somatic cells into pluripotent cells remain largely unknown. Using fibroblasts and induced pluripotent stem cells (iPSCs) at different stages of reprogramming, we performed RNA transcriptome sequencing (RNA-Seq) to identify lncRNAs that are differentially-expressed in association with pluripotency. An RNA reverse transcription-associated trap sequencing (RAT-seq) approach was then utilized to generate a database to map the regulatory element network for lncRNA candidates. Integration of these datasets can facilitate the identification of functional lncRNAs that are associated with reprogramming. Identification of lncRNAs that regulate pluripotency may lead to new strategies for enhancing iPSC induction in regenerative medicine.
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Affiliation(s)
- Zhonghua Du
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Lin Jia
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yichen Wang
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Cong Wang
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Xue Wen
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Jingcheng Chen
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yanbo Zhu
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Dehai Yu
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Lei Zhou
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Naifei Chen
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Shilin Zhang
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Ilkay Celik
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Sujun Gao
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Songling Zhang
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Li
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
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48
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Li W, Ren Y, Si Y, Wang F, Yu J. Long non-coding RNAs in hematopoietic regulation. CELL REGENERATION 2018; 7:27-32. [PMID: 30671227 PMCID: PMC6326246 DOI: 10.1016/j.cr.2018.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/11/2018] [Accepted: 08/21/2018] [Indexed: 02/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) have crucial roles via tethering with DNA, RNA or protein in diverse biological processes. These lncRNA-mediated interactions enhance gene regulatory networks and modulate a wide range of downstream genes. It has been demonstrated that several lncRNAs act as key regulators in hematopoiesis. This review highlights the roles of lncRNAs in normal hematopoietic development and discusses how lncRNA dysregulation correlates with disease prognoses and phenotypes.
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Affiliation(s)
- Weiqian Li
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yue Ren
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanmin Si
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
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49
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Huang H, Sun J, Sun Y, Wang C, Gao S, Li W, Hu JF. Long noncoding RNAs and their epigenetic function in hematological diseases. Hematol Oncol 2018; 37:15-21. [PMID: 30052285 DOI: 10.1002/hon.2534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022]
Abstract
Recent discoveries demonstrate the importance of long noncoding RNA (lncRNA) in the regulation of multiple major processes impacting development, differentiation, and metastasis of hematological diseases through epigenetic mechanisms. In contrast to genetic changes, epigenetic modification does not modify genes but is frequently reversible, thus providing opportunities for targeted treatment using specific inhibitors. In this review, we will summarize the function and epigenetic mechanism of lncRNA in malignant hematologic diseases.
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Affiliation(s)
- Hanying Huang
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jingnan Sun
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Yunpeng Sun
- Cardiovascular Surgery Department, First Hospital of Jilin University, Changchun, Jilin, China
| | - Cong Wang
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Sujun Gao
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ji-Fan Hu
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
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50
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Tian X, Ma J, Wang T, Tian J, Zheng Y, Peng R, Wang Y, Zhang Y, Mao L, Xu H, Wang S. Long non-coding RNA RUNXOR accelerates MDSC-mediated immunosuppression in lung cancer. BMC Cancer 2018; 18:660. [PMID: 29914443 PMCID: PMC6006856 DOI: 10.1186/s12885-018-4564-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022] Open
Abstract
Background RUNX1 overlapping RNA (RUNXOR) is a long non-coding RNA that has been indicated as a key regulator in the development of myeloid cells by targeting runt-related transcription factor 1 (RUNX1). Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of cells consisting of immature granulocytes and monocytes with immunosuppression. However, the impact of lncRNA RUNXOR on the development of MDSCs remains unknown. Methods Both the expressions of RUNXOR and RUNX1 in the peripheral blood were measured by qRT-PCR. Human MDSCs used in this study were isolated from tumor tissue of patients with lung cancer by FCM or induced from PBMCs of healthy donors with IL-1β + GM-CSF. Specific siRNA was used to knockdown the expression of RUNXOR in MDSCs. Results In this study, we found that the lncRNA RUNXOR was upregulated in the peripheral blood of lung cancer patients. In addition, as a target gene of RUNXOR, the expression of RUNX1 was downregulated in lung cancer patients. Finally, the expression of RUNXOR was higher in MDSCs isolated from the tumor tissues of lung cancer patients compared with cells from adjacent tissue. In addition, RUNXOR knockdown decreased Arg1 expression in MDSCs. Conclusions Based on our findings, it is illustrated that RUNXOR is significantly associated with the immunosuppression induced by MDSCs in lung cancer patients and may be a target of anti-tumor therapy.
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Affiliation(s)
- Xinyu Tian
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212012, China.,Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jie Ma
- Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ting Wang
- Department of Laboratory Medicine, Jiangsu Cancer Hospital, Nanjing, China
| | - Jie Tian
- Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yu Zheng
- Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Rongrong Peng
- Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yungang Wang
- Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yue Zhang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212012, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212012, China.
| | - Huaxi Xu
- Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212012, China. .,Institute of Laboratory Medicine, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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