1
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Gupta S, Silveira DA, Lorenzoni PR, Mombach JCM, Hashimoto RF. LncRNA PTENP1/miR-21/PTEN Axis Modulates EMT and Drug Resistance in Cancer: Dynamic Boolean Modeling for Cell Fates in DNA Damage Response. Int J Mol Sci 2024; 25:8264. [PMID: 39125832 PMCID: PMC11311614 DOI: 10.3390/ijms25158264] [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: 07/05/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
It is well established that microRNA-21 (miR-21) targets phosphatase and tensin homolog (PTEN), facilitating epithelial-to-mesenchymal transition (EMT) and drug resistance in cancer. Recent evidence indicates that PTEN activates its pseudogene-derived long non-coding RNA, PTENP1, which in turn inhibits miR-21. However, the dynamics of PTEN, miR-21, and PTENP1 in the DNA damage response (DDR) remain unclear. Thus, we propose a dynamic Boolean network model by integrating the published literature from various cancers. Our model shows good agreement with the experimental findings from breast cancer, hepatocellular carcinoma (HCC), and oral squamous cell carcinoma (OSCC), elucidating how DDR activation transitions from the intra-S phase to the G2 checkpoint, leading to a cascade of cellular responses such as cell cycle arrest, senescence, autophagy, apoptosis, drug resistance, and EMT. Model validation underscores the roles of PTENP1, miR-21, and PTEN in modulating EMT and drug resistance. Furthermore, our analysis reveals nine novel feedback loops, eight positive and one negative, mediated by PTEN and implicated in DDR cell fate determination, including pathways related to drug resistance and EMT. Our work presents a comprehensive framework for investigating cellular responses following DDR, underscoring the therapeutic potential of targeting PTEN, miR-21, and PTENP1 in cancer treatment.
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Affiliation(s)
- Shantanu Gupta
- Instituto de Matemática e Estatística, Departamento de Ciência da Computação, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, SP, Brazil;
| | | | - Pedro R. Lorenzoni
- Departamento de Física, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (P.R.L.); (J.C.M.M.)
| | - Jose Carlos M. Mombach
- Departamento de Física, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (P.R.L.); (J.C.M.M.)
| | - Ronaldo F. Hashimoto
- Instituto de Matemática e Estatística, Departamento de Ciência da Computação, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, SP, Brazil;
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2
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Umapathy VR, Natarajan PM, Swamikannu B. Molecular and Therapeutic Roles of Non-Coding RNAs in Oral Cancer-A Review. Molecules 2024; 29:2402. [PMID: 38792263 PMCID: PMC11123887 DOI: 10.3390/molecules29102402] [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: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Oral cancer (OC) is among the most common malignancies in the world. Despite advances in therapy, the worst-case scenario for OC remains metastasis, with a 50% survival rate. Therefore, it is critical to comprehend the pathophysiology of the condition and to create diagnostic and treatment plans for OC. The development of high-throughput genome sequencing has revealed that over 90% of the human genome encodes non-coding transcripts, or transcripts that do not code for any proteins. This paper describes the function of these different kinds of non-coding RNAs (ncRNAs) in OC as well as their intriguing therapeutic potential. The onset and development of OC, as well as treatment resistance, are linked to dysregulated ncRNA expression. These ncRNAs' potentially significant roles in diagnosis and prognosis have been suggested by their differing expression in blood or saliva. We have outlined every promising feature of ncRNAs in the treatment of OC in this study.
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Affiliation(s)
- Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Dr. M.G.R. Educational and Research Institute, Thai Moogambigai Dental College and Hospital, Chennai 600107, Tamil Nadu, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Centre of Medical and Bio-Allied Health Sciences and Research Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Bhuminathan Swamikannu
- Department of Prosthodontics, Sree Balaji Dental College and Hospital, Pallikaranai, BIHER, Chennai 600100, Tamil Nadu, India;
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3
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Gupta S, Silveira DA, Piedade GP, Ostrowski MP, Mombach JCM, Hashimoto RF. A dynamic Boolean network reveals that the BMI1 and MALAT1 axis is associated with drug resistance by limiting miR-145-5p in non-small cell lung cancer. Noncoding RNA Res 2024; 9:185-193. [PMID: 38125755 PMCID: PMC10730431 DOI: 10.1016/j.ncrna.2023.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/23/2023] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) are often treated with chemotherapy. Poor clinical response and the onset of chemoresistance limit the anti-tumor benefits of drugs such as cisplatin. According to recent research, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA related to cisplatin resistance in NSCLC. Furthermore, MALAT1 targets microRNA-145-5p (miR-145), which activates Krüppel-like factor 4 (KLF4) in associated cell lines. B lymphoma Mo-MLV insertion region 1 homolog (BMI1), on the other hand, inhibits miR-145 expression, which stimulates Specificity protein 1 (Sp1) to trigger the epithelial-mesenchymal transition (EMT) process in pemetrexed-resistant NSCLC cells. The interplay between these molecules in drug resistance is still unclear. Therefore, we propose a dynamic Boolean network that can encapsulate the complexity of these drug-resistant molecules. Using published clinical data for gain or loss-of-function perturbations, our network demonstrates reasonable agreement with experimental observations. We identify four new positive circuits: miR-145/Sp1/MALAT1, BMI1/miR-145/Myc, KLF4/p53/miR-145, and miR-145/Wip1/p38MAPK/p53. Notably, miR-145 emerges as a central player in these regulatory circuits, underscoring its pivotal role in NSCLC drug resistance. Our circuit perturbation analysis further emphasizes the critical involvement of these new circuits in drug resistance for NSCLC. In conclusion, targeting MALAT1 and BMI1 holds promise for overcoming drug resistance, while activating miR-145 represents a potential strategy to significantly reduce drug resistance in NSCLC.
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Affiliation(s)
- Shantanu Gupta
- Instituto de Matemática e Estatística, Departamento de Ciência da Computação, Universidade de São Paulo, Rua do Matão 1010, 05508-090, São Paulo, SP, Brazil
| | - Daner A. Silveira
- Children's Cancer Institute, Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel P.S. Piedade
- Instituto de Matemática e Estatística, Departamento de Ciência da Computação, Universidade de São Paulo, Rua do Matão 1010, 05508-090, São Paulo, SP, Brazil
| | - Miguel P. Ostrowski
- Instituto de Matemática e Estatística, Departamento de Ciência da Computação, Universidade de São Paulo, Rua do Matão 1010, 05508-090, São Paulo, SP, Brazil
| | - José Carlos M. Mombach
- Departamento de Física, Universidade Federal de Santa Maria, Santa Maria, 97105-900, RS, Brazil
| | - Ronaldo F. Hashimoto
- Instituto de Matemática e Estatística, Departamento de Ciência da Computação, Universidade de São Paulo, Rua do Matão 1010, 05508-090, São Paulo, SP, Brazil
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4
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Stieg DC, Wang Y, Liu LZ, Jiang BH. ROS and miRNA Dysregulation in Ovarian Cancer Development, Angiogenesis and Therapeutic Resistance. Int J Mol Sci 2022; 23:ijms23126702. [PMID: 35743145 PMCID: PMC9223852 DOI: 10.3390/ijms23126702] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/05/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
The diverse repertoires of cellular mechanisms that progress certain cancer types are being uncovered by recent research and leading to more effective treatment options. Ovarian cancer (OC) is among the most difficult cancers to treat. OC has limited treatment options, especially for patients diagnosed with late-stage OC. The dysregulation of miRNAs in OC plays a significant role in tumorigenesis through the alteration of a multitude of molecular processes. The development of OC can also be due to the utilization of endogenously derived reactive oxygen species (ROS) by activating signaling pathways such as PI3K/AKT and MAPK. Both miRNAs and ROS are involved in regulating OC angiogenesis through mediating multiple angiogenic factors such as hypoxia-induced factor (HIF-1) and vascular endothelial growth factor (VEGF). The NAPDH oxidase subunit NOX4 plays an important role in inducing endogenous ROS production in OC. This review will discuss several important miRNAs, NOX4, and ROS, which contribute to therapeutic resistance in OC, highlighting the effective therapeutic potential of OC through these mechanisms.
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Affiliation(s)
- David C. Stieg
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; (D.C.S.); (L.-Z.L.)
| | - Yifang Wang
- Department of Pathology, Anatomy & Cell Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Ling-Zhi Liu
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; (D.C.S.); (L.-Z.L.)
| | - Bing-Hua Jiang
- Department of Pathology, Anatomy & Cell Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA;
- Correspondence:
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5
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Ravi S, Alencar AM, Arakelyan J, Xu W, Stauber R, Wang CCI, Papyan R, Ghazaryan N, Pereira RM. An Update to Hallmarks of Cancer. Cureus 2022; 14:e24803. [PMID: 35686268 PMCID: PMC9169686 DOI: 10.7759/cureus.24803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2022] [Indexed: 12/03/2022] Open
Abstract
In the last decade, there has been remarkable progress in research toward understanding and refining the hallmarks of cancer. In this review, we propose a new hallmark - "pro-survival autophagy." The importance of pro-survival autophagy is well established in tumorigenesis, as it is related to multiple steps in cancer progression and vital for some cancers. Autophagy is a potential anti-cancer therapeutic target. For this reason, autophagy is a good candidate as a new hallmark of cancer. We describe two enabling characteristics that play a major role in enabling cells to acquire the hallmarks of cancer - "tumor-promoting microenvironment and macroenvironment" and "cancer epigenetics, genome instability and mutation." We also discuss the recent updates, therapeutic and prognostic implications of the eight hallmarks of cancer described by Hanahan et al. in 2011. Understanding these hallmarks and enabling characteristics is key not only to developing new ways to treat cancer efficiently but also to exploring options to overcome cancer resistance to treatment.
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Affiliation(s)
- Swapna Ravi
- Department of Medicine, St. Luke's Hospital, Duluth, USA
| | - Antonio M Alencar
- Department of Medical Oncology, Hospital Universitário da Universidade Federal do Maranhão, Hospital São Domingos, São Luís, BRA
| | - Jemma Arakelyan
- Department of Oncology/Solid Tumors, Yerevan State Medical University, Hematology Center After Prof. R. Yeolyan, Yerevan, ARM
| | - Weihao Xu
- Department of Business Development, Harbour BioMed, Boston, USA
| | - Roberta Stauber
- Department of Oncology, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, BRA
| | - Cheng-Chi I Wang
- Department of Research and Development, Beltie Bio, Inc, San Diego, USA
| | - Ruzanna Papyan
- Department of Pediatric Oncology and Hematology, Yerevan State Medical University, Pediatric Center and Blood Disorders Center of Armenia, Yerevan, ARM
| | - Narine Ghazaryan
- Department of Molecular Biology, L.A. Orbeli Institute of Physiology National Academy of Sciences, Republic of Armenia (NAS RA) Hematology Center After Prof. R. Yeolyan, Yerevan, ARM
| | - Rosalina M Pereira
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, USA
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6
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Gupta S, Silveira DA, Hashimoto RF, Mombach JCM. A Boolean Model of the Proliferative Role of the lncRNA XIST in Non-Small Cell Lung Cancer Cells. BIOLOGY 2022; 11:biology11040480. [PMID: 35453680 PMCID: PMC9024590 DOI: 10.3390/biology11040480] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/12/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
Abstract
The long non-coding RNA X inactivate-specific transcript (lncRNA XIST) has been verified as an oncogenic gene in non-small cell lung cancer (NSCLC) whose regulatory role is largely unknown. The important tumor suppressors, microRNAs: miR-449a and miR-16 are regulated by lncRNA XIST in NSCLC, these miRNAs share numerous common targets and experimental evidence suggests that they synergistically regulate the cell-fate regulation of NSCLC. LncRNA XIST is known to sponge miR-449a and miR-34a, however, the regulatory network connecting all these non-coding RNAs is still unknown. Here we propose a Boolean regulatory network for the G1/S cell cycle checkpoint in NSCLC contemplating the involvement of these non-coding RNAs. Model verification was conducted by comparison with experimental knowledge from NSCLC showing good agreement. The results suggest that miR-449a regulates miR-16 and p21 activity by targeting HDAC1, c-Myc, and the lncRNA XIST. Furthermore, our circuit perturbation simulations show that five circuits are involved in cell fate determination between senescence and apoptosis. The model thus allows pinpointing the direct cell fate mechanisms of NSCLC. Therefore, our results support that lncRNA XIST is an attractive target of drug development in tumor growth and aggressive proliferation of NSCLC, and promising results can be achieved through tumor suppressor miRNAs.
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Affiliation(s)
- Shantanu Gupta
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, SP, Brazil;
- Correspondence: (S.G.); (J.C.M.M.); Tel.: +55-11-30916135 (S.G.); +55-55-32209521 (J.C.M.M.)
| | - Daner A. Silveira
- Departamento de Física, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil;
| | - Ronaldo F. Hashimoto
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, SP, Brazil;
| | - Jose Carlos M. Mombach
- Departamento de Física, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil;
- Correspondence: (S.G.); (J.C.M.M.); Tel.: +55-11-30916135 (S.G.); +55-55-32209521 (J.C.M.M.)
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7
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Dynamical Analysis of a Boolean Network Model of the Oncogene Role of lncRNA ANRIL and lncRNA UFC1 in Non-Small Cell Lung Cancer. Biomolecules 2022; 12:biom12030420. [PMID: 35327612 PMCID: PMC8946683 DOI: 10.3390/biom12030420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) such as ANRIL and UFC1 have been verified as oncogenic genes in non-small cell lung cancer (NSCLC). It is well known that the tumor suppressor microRNA-34a (miR-34a) is downregulated in NSCLC. Furthermore, miR-34a induces senescence and apoptosis in breast, glioma, cervical cancer including NSCLC by targeting Myc. Recent evidence suggests that these two lncRNAs act as a miR-34a sponge in corresponding cancers. However, the biological functions between these two non-coding RNAs (ncRNAs) have not yet been studied in NSCLC. Therefore, we present a Boolean model to analyze the gene regulation between these two ncRNAs in NSCLC. We compared our model to several experimental studies involving gain- or loss-of-function genes in NSCLC cells and achieved an excellent agreement. Additionally, we predict three positive circuits involving miR-34a/E2F1/ANRIL, miR-34a/E2F1/UFC1, and miR-34a/Myc/ANRIL. Our circuit- perturbation analysis shows that these circuits are important for regulating cell-fate decisions such as senescence and apoptosis. Thus, our Boolean network permits an explicit cell-fate mechanism associated with NSCLC. Therefore, our results support that ANRIL and/or UFC1 is an attractive target for drug development in tumor growth and aggressive proliferation of NSCLC, and that a valuable outcome can be achieved through the miRNA-34a/Myc pathway.
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8
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Finite-Time Set Reachability of Probabilistic Boolean Multiplex Control Networks. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12020883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study focuses on the finite-time set reachability of probabilistic Boolean multiplex control networks (PBMCNs). Firstly, based on the state transfer graph (STG) reconstruction technique, the PBMCNs are extended to random logic dynamical systems. Then, a necessary and sufficient condition for the finite-time set reachability of PBMCNs is obtained. Finally, the obtained results are effectively illustrated by an example.
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9
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Zhang L, Nguyen LXT, Chen YC, Wu D, Cook GJ, Hoang DH, Brewer CJ, He X, Dong H, Li S, Li M, Zhao D, Qi J, Hua WK, Cai Q, Carnahan E, Chen W, Wu X, Swiderski P, Rockne RC, Kortylewski M, Li L, Zhang B, Marcucci G, Kuo YH. Targeting miR-126 in inv(16) acute myeloid leukemia inhibits leukemia development and leukemia stem cell maintenance. Nat Commun 2021; 12:6154. [PMID: 34686664 PMCID: PMC8536759 DOI: 10.1038/s41467-021-26420-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/05/2021] [Indexed: 12/21/2022] Open
Abstract
Acute myeloid leukemia (AML) harboring inv(16)(p13q22) expresses high levels of miR-126. Here we show that the CBFB-MYH11 (CM) fusion gene upregulates miR-126 expression through aberrant miR-126 transcription and perturbed miR-126 biogenesis via the HDAC8/RAN-XPO5-RCC1 axis. Aberrant miR-126 upregulation promotes survival of leukemia-initiating progenitors and is critical for initiating and maintaining CM-driven AML. We show that miR-126 enhances MYC activity through the SPRED1/PLK2-ERK-MYC axis. Notably, genetic deletion of miR-126 significantly reduces AML rate and extends survival in CM knock-in mice. Therapeutic depletion of miR-126 with an anti-miR-126 (miRisten) inhibits AML cell survival, reduces leukemia burden and leukemia stem cell (LSC) activity in inv(16) AML murine and xenograft models. The combination of miRisten with chemotherapy further enhances the anti-leukemia and anti-LSC activity. Overall, this study provides molecular insights for the mechanism and impact of miR-126 dysregulation in leukemogenesis and highlights the potential of miR-126 depletion as a therapeutic approach for inv(16) AML. miR-126 is highly expressed in inv(16) Acute myeloid leukemia (AML) but its role is unclear. Here, the authors show that the aberrant expression of miR-126 in inv(16) AML is directly due to the CBFB-MYH11 fusion gene and that it can promote AML development and leukemia stem cell maintenance, highlighting miR-126 as a therapeutic target for inv(16) AML patients
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Affiliation(s)
- Lianjun Zhang
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Le Xuan Truong Nguyen
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Ying-Chieh Chen
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Dijiong Wu
- Department of Hematology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310006, China
| | - Guerry J Cook
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Dinh Hoa Hoang
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Casey J Brewer
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Xin He
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Haojie Dong
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Shu Li
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Man Li
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Dandan Zhao
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Jing Qi
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Wei-Kai Hua
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Qi Cai
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Emily Carnahan
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Wei Chen
- Integrated Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrated Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Piotr Swiderski
- Department of Molecular Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Russell C Rockne
- Department of Computational and Quantitative Medicine, Division of Mathematical Oncology, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Marcin Kortylewski
- Department of Immuno-oncology, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Ling Li
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Bin Zhang
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA
| | - Ya-Huei Kuo
- Gehr Family Center for Leukemia Research, Department of Hematological Malignancies Translational Science, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, 91010, USA.
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10
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Schott J, Reitter S, Lindner D, Grosser J, Bruer M, Shenoy A, Geiger T, Mathes A, Dobreva G, Stoecklin G. Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density. Nat Methods 2021; 18:1068-1074. [PMID: 34480152 DOI: 10.1038/s41592-021-01250-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/23/2021] [Indexed: 01/21/2023]
Abstract
In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its association with ribosomes, which was calculated to be 20-22 min for bulk mRNA. In mouse embryonic stem cells, nRibo-Seq revealed an even stronger lag of 35-38 min in ribosome loading. After stimulation of macrophages with lipopolysaccharide, the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments, which gives rise to distorted RD measurements under conditions where mRNA amounts are far from steady-state expression. As a result, we demonstrate that transcriptional changes affect RD in a passive way.
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Affiliation(s)
- Johanna Schott
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. .,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany.
| | - Sonja Reitter
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Doris Lindner
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Jan Grosser
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Marius Bruer
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Anjana Shenoy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Geiger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arthur Mathes
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Georg Stoecklin
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
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11
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Swellam M, Bakr NM, El Magdoub HM, Hamza MS, Ezz El Arab LR. Emerging role of miRNAs as liquid biopsy markers for prediction of glioblastoma multiforme prognosis. J Mol Neurosci 2020; 71:836-844. [PMID: 32989634 DOI: 10.1007/s12031-020-01706-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/07/2020] [Indexed: 01/01/2023]
Abstract
Serum miRNAs (miRs) have gained consideration as encouraging molecular markers for cancer diagnosis and prediction of prognosis. The authors aimed to identify the exact role of miR-17-5p, miR-125b, and miR-221 among glioblastoma multiforme (GBM) patients before and after standard treatment, and correlate their expression with survival pattern. The study included 25 GBM patients and 20 healthy controls. Serum miR-17-5p, miR-125b, and miR-221 expression were analyzed before and after treatment using quantitative real-time polymerase chain reaction (qPCR). The diagnostic efficacy for the tested miRs was evaluated using the receiver operating characteristic (ROC) curve, and the relation of miRs expression versus clinical criteria for GBM was assessed. Patients' survival patterns were examined versus miRs expression levels. A significant difference was reported between miRs expression among the enrolled individuals. Both miR-17-5p and miR-221 reported significant elevations in GBM patients who: are above 60 years old, underwent biopsy resection, have a non-frontal lesion, with tumor size above 5 cm, and with performance status equals 2 according to the Eastern Cooperative Oncology Group (ECOG) Performance Status. With regard to miR-125b, a significant difference was detected according to surgery strategy, primary lesion of the tumor, and ECOG status. MiRs levels were significantly decreased for GBM patients after treatment. Survival patterns demonstrated an increase in miR-17-5p, miR-125b, and miR-221 in GBM patients with worse progression-free survival and among those with worse overall survival. Detection of serum miR-17-5p, miR-125b, and miR-221 aids in the prediction of prognosis and response to treatment strategy for GBM patients.
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Affiliation(s)
- Menha Swellam
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, Dokki, Egypt.,High Throughput Molecular and Genetic Laboratory, Centers of Excellence for Advanced Sciences, National Research Centre, Giza, Dokki, Egypt
| | - Noha M Bakr
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, Dokki, Egypt.,High Throughput Molecular and Genetic Laboratory, Centers of Excellence for Advanced Sciences, National Research Centre, Giza, Dokki, Egypt
| | - Hekmat M El Magdoub
- Biochemistry Department, Faculty of Pharmacy, Translational Research Unit, Misr International University, Cairo, Egypt.
| | - Marwa S Hamza
- Clinical Pharmacy Practice Department, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo, Egypt.,The Center for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo, Egypt
| | - Lobna R Ezz El Arab
- Clinical Oncology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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12
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Gupta S, Silveira DA, Mombach JCM. Towards DNA-damage induced autophagy: A Boolean model of p53-induced cell fate mechanisms. DNA Repair (Amst) 2020; 96:102971. [PMID: 32987354 DOI: 10.1016/j.dnarep.2020.102971] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/28/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022]
Abstract
How a cell determines a given phenotype upon damaged DNA is an open problem. Cell fate decisions happen at cell cycle checkpoints and it is becoming clearer that the p53 pathway is a major regulator of cell fate decisions involving apoptosis or senescence upon DNA damage, especially at G1/S. However, recent results suggest that this pathway is also involved in autophagy induction upon DNA damage. To our knowledge, in this work we propose the first model of the DNA damage-induced G1/S checkpoint contemplating the decision between three phenotypes: apoptosis, senescence, and autophagy. The Boolean model is proposed based on experiments with U87 glioblastoma cells using the transfection of miR-16 that can induce a DNA damage response. The wild-type case of the model shows that DNA damage induces the checkpoint and the coexistence of the three phenotypes (tristable dynamics), each with a different probability. We also predict that the positive feedback involving ATM, miR-16, and Wip1 has an influence on the tristable state. The model predictions were compared to experiments of gain and loss of function in other three different cell lines (MCF-7, A549, and U2OS) presenting agreement. For p53-deficient cell lines such as HeLa, H1299, and PC-3, our model contemplates the experimental observation that the alternative AMPK pathway can compensate this deficiency. We conclude that at the G1/S checkpoint the p53 pathway (or, in its absence, the AMPK pathway) can regulate the induction of different phenotypes in a stochastic manner in the U87 cell line and others.
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Affiliation(s)
- Shantanu Gupta
- Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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13
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García-Martínez A, López-Muñoz B, Fajardo C, Cámara R, Lamas C, Silva-Ortega S, Aranda I, Picó A. Increased E2F1 mRNA and miR-17-5p Expression Is Correlated to Invasiveness and Proliferation of Pituitary Neuroendocrine Tumours. Diagnostics (Basel) 2020; 10:diagnostics10040227. [PMID: 32316225 PMCID: PMC7235816 DOI: 10.3390/diagnostics10040227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/12/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022] Open
Abstract
miR-17-5p and E2F1 have been described as deregulated in cancer, but they have scarcely been studied in pituitary neuroendocrine tumours (PitNETs). This study evaluates the relationship of E2F1 and miR-17-5p with the invasiveness and proliferation of PitNETs. In this cross-sectional descriptive study, we evaluated the expression of E2F1, MYC, and miR-17-5p by quantitative real time PCR analysis in 60 PitNETs: 29 gonadotroph (GT), 15 functioning somatotroph (ST), and 16 corticotroph (CT) tumours, of which 8 were silent (sCT). The clinical data were collected from the Spanish Molecular Register of Pituitary Adenomas (REMAH) database. We defined invasiveness according to the Knosp classification and proliferation according to a molecular expression of Ki-67 ≥ 2.59. E2F1 was more expressed in invasive than in non-invasive tumours in the whole series (p = 0.004) and in STs (p = 0.01). In addition, it was overexpressed in the silent subtypes (GTs and sCTs; all macroadenomas) and normoexpressed in the functioning ones (fCTs and STs; some microadenomas). miR-17-5p was more expressed in proliferative than in non-proliferative tumours (p = 0.041) in the whole series but not by subtypes. Conclusions: Our study suggests that in PitNETs, E2F1 could be a good biomarker of invasiveness, and miR-17-5p of proliferation, helping the clinical management of these tumours.
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Affiliation(s)
- Araceli García-Martínez
- Research Laboratory, Hospital General Universitario de Alicante-Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain;
| | - Beatriz López-Muñoz
- Department of Endocrinology & Nutrition, Hospital General Universitario de Alicante -ISABIAL, 03010 Alicante, Spain;
| | - Carmen Fajardo
- Department of Endocrinology and Nutrition, Hospital La Ribera, Alzira, 46600 Valencia, Spain;
| | - Rosa Cámara
- Department of Endocrinology & Nutrition, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Cristina Lamas
- Department of Endocrinology & Nutrition, Hospital General Universitario de Albacete, 02006 Albacete, Spain;
| | - Sandra Silva-Ortega
- Department of Pathology, Hospital General Universitario de Alicante -ISABIAL, 03010 Alicante, Spain; (S.S.-O.); (I.A.)
| | - Ignacio Aranda
- Department of Pathology, Hospital General Universitario de Alicante -ISABIAL, 03010 Alicante, Spain; (S.S.-O.); (I.A.)
| | - Antonio Picó
- Department of Endocrinology & Nutrition, Hospital General Universitario de Alicante, Miguel Hernández University, 03010 Alicante, Spain
- Correspondence:
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14
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Zaheer U, Faheem M, Qadri I, Begum N, Yassine HM, Al Thani AA, Mathew S. Expression profile of MicroRNA: An Emerging Hallmark of Cancer. Curr Pharm Des 2020; 25:642-653. [PMID: 30914015 DOI: 10.2174/1386207322666190325122821] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/22/2019] [Indexed: 12/28/2022]
Abstract
MicroRNA (miRNAs), a class of small, endogenous non-coding RNA molecules of about 21-24 nucleotides in length, have unraveled a new modulatory network of RNAs that form an additional level of posttranscriptional gene regulation by targeting messenger RNAs (mRNAs). These miRNAs possess the ability to regulate gene expression by modulating the stability of mRNAs, controlling their translation rates, and consequently regulating protein synthesis. Substantial experimental evidence established the involvement of miRNAs in most biological processes like growth, differentiation, development, and metabolism in mammals including humans. An aberrant expression of miRNAs has been implicated in several pathologies, including cancer. The association of miRNAs with tumor growth, development, and metastasis depicts their potential as effective diagnostic and prognostic biomarkers. Furthermore, exploitation of the role of different miRNAs as oncogenes or tumor suppressors has aided in designing several miRNA-based therapeutic approaches for treating cancer patients whose clinical trials are underway. In this review, we aim to summarize the biogenesis of miRNAs and the dysregulations in these pathways that result in various pathologies and in some cases, resistance to drug treatment. We provide a detailed review of the miRNA expression signatures in different cancers along with their diagnostic and prognostic utility. Furthermore, we elaborate on the potential employment of miRNAs to enhance cancer cell apoptosis, regress tumor progression and even overcome miRNA-induced drug resistance.
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Affiliation(s)
- Uzma Zaheer
- Postgraduate Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Muhammed Faheem
- Department of Biology, King Abdul Aziz University, 80216 Jeddah, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biology, King Abdul Aziz University, 80216 Jeddah, Saudi Arabia
| | - Nargis Begum
- Postgraduate Department of Biotechnology, Jamal Mohamed College, Trichy, India
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, Doha, Qatar.,Department of Biomedical Science, College of Health Science, Qatar University, Doha, Qatar
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, Doha, Qatar
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15
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Nanotechnology, in silico and endocrine-based strategy for delivering paclitaxel and miRNA: Prospects for the therapeutic management of breast cancer. Semin Cancer Biol 2019; 69:109-128. [PMID: 31891780 DOI: 10.1016/j.semcancer.2019.12.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/06/2019] [Accepted: 12/25/2019] [Indexed: 02/07/2023]
Abstract
Breast cancer is one of the most prevalent and reoccurring cancers and the second most common reason of death in women. Despite advancements in therapeutic strategies for breast cancer, early tumor recurrence and metastasis in patients indicate resistance to chemotherapeutic medicines, such as paclitaxel due to the abnormal expression of ER and EGF2 in breast cancer cells. Therefore, the development of alternatives to paclitaxel is urgently needed to overcome challenges involving drug resistance. An increasing number of studies has revealed miRNAs as novel natural alternative substances that play a crucial role in regulating several physiological processes and have a close, adverse association with several diseases, including breast cancer. Due to the therapeutic potential of miRNA and paclitaxel in cancer research, the current review focuses on the differential roles of various miRNAs in breast cancer development and treatment. miRNA delivery to a specific target site, the development of paclitaxel and miRNA formulations, and nanotechnological strategies for the delivery of nanopaclitaxel in the management of breast cancer are discussed. These strategies involve improving the cellular uptake and bioavailability and reducing the toxicity of free paclitaxel to achieve accumulation tumor site. Furthermore, a molecular docking study was performed to ascertain the enhanced anticancer activity of the nanoformulation of ANG1005 and Abraxane. An in silico analysis revealed that ANG1005 and Abraxane nanoformulations have superior and significantly enhanced interactions with the proteins α-tubulin and Bcl-2. Therefore, ANG1005 and Abraxane may be more suitable in the therapeutic management of breast cancer than the existing free paclitaxel. miRNAs can revert abnormal gene expression to normalcy; since miRNAs serve as tumor suppressors. Therefore, restoration of particular miRNAs levels as a replacement therapy may be an effective endocrine potential strategy for treating ER positive/ negative breast cancers.
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16
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Zou D, Dong L, Li C, Yin Z, Rao S, Zhou Q. The m 6A eraser FTO facilitates proliferation and migration of human cervical cancer cells. Cancer Cell Int 2019; 19:321. [PMID: 31827395 PMCID: PMC6888952 DOI: 10.1186/s12935-019-1045-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background Since FTO was recognized as the first m6A demethylase, the understanding of its biological function has been widely expanded. However, the role of FTO in cervical cancer tumorigenesis remains unclear. Methods In this study, we first analyzed the expression of FTO in two independent human cancer datasets and evaluated the correlation between FTO level and cervical cancer progression. Using small hairpin RNA technology, we explored the function of FTO in cervical cancer cell line Hela and SiHa cells, respectively. We then determined the FTO targets by performing transcriptional profile with FTO deficient and competent Hela cells, and finally validated these targets with ribosome profiling and functional rescue experiments. Results Our data suggested that FTO was frequently overexpressed in human cervical cancer tissues and highly correlated with cervical cancer progression. FTO serves as an oncogenic regulator for cervical cancer cells' proliferation and migration which is vastly depended on its demethylase activity. Mechanistically, FTO interacts with transcripts of E2F1 and Myc, inhibition of FTO significantly impairs the translation efficiency of E2F1 and Myc, however, either overexpress E2F1 or Myc sufficiently compensates the FTO deficiency which decreases cell proliferation and migration. Conclusions Our study indicates that FTO plays important oncogenic role in regulating cervical cancer cells' proliferation and migration via controlling m6A modification of E2F1 and Myc transcripts. FTO represents a potential drug candidate for cervical cancer therapy.
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Affiliation(s)
- Dongling Zou
- 1Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030 China
| | - Lei Dong
- 2Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA USA
| | - Chenying Li
- 3Department of Hematology, School of Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003 China
| | - Zhe Yin
- 1Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030 China
| | - Shuan Rao
- 4Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Qi Zhou
- 1Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030 China
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17
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Robaina MC, Mazzoccoli L, Klumb CE. Germinal Centre B Cell Functions and Lymphomagenesis: Circuits Involving MYC and MicroRNAs. Cells 2019; 8:E1365. [PMID: 31683676 PMCID: PMC6912346 DOI: 10.3390/cells8111365] [Citation(s) in RCA: 10] [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: 08/06/2019] [Revised: 09/30/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The transcription factor MYC regulates several biological cellular processes, and its target gene network comprises approximately 15% of all human genes, including microRNAs (miRNAs), that also contribute to MYC regulatory activity. Although miRNAs are emerging as key regulators of immune functions, the specific roles of miRNAs in the regulation/dysregulation of germinal centre B-cells and B-cell lymphomas are still being uncovered. The regulatory network that integrates MYC, target genes and miRNAs is a field of intense study, highlighting potential pathways to be explored in the context of future clinical approaches. METHODS The scientific literature that is indexed in PUBMED was consulted for publications involving MYC and miRNAs with validated bioinformatics analyses or experimental protocols. Additionally, seminal studies on germinal centre B-cell functions and lymphomagenesis were reported. CONCLUSIONS This review summarizes the interactions between MYC and miRNAs through regulatory loops and circuits involving target genes in germinal centre B-cell lymphomas with MYC alterations. Moreover, we provide an overview of the understanding of the regulatory networks between MYC and miRNAs, highlighting the potential implication of this approach for the comprehension of germinal centre B-cell lymphoma pathogenesis. Therefore, circuits involving MYC, target genes and miRNAs provide novel insight into lymphomagenesis that could be useful for new improved therapeutic strategies.
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Affiliation(s)
- Marcela Cristina Robaina
- Programa de Pesquisa em Hemato-Oncologia Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, CEP: 20230-130, Brazil.
| | - Luciano Mazzoccoli
- Programa de Pesquisa em Hemato-Oncologia Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, CEP: 20230-130, Brazil.
| | - Claudete Esteves Klumb
- Programa de Pesquisa em Hemato-Oncologia Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, CEP: 20230-130, Brazil.
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18
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Filip D, Mraz M. The role of MYC in the transformation and aggressiveness of ‘indolent’ B-cell malignancies. Leuk Lymphoma 2019; 61:510-524. [DOI: 10.1080/10428194.2019.1675877] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Daniel Filip
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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19
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Gupta S, Silveira DA, Mombach JCM. ATM/miR‐34a‐5p axis regulates a p21‐dependent senescence‐apoptosis switch in non‐small cell lung cancer: a Boolean model of G1/S checkpoint regulation. FEBS Lett 2019; 594:227-239. [DOI: 10.1002/1873-3468.13615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/16/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Shantanu Gupta
- Department of Physics Universidade Federal de Santa Maria Brazil
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20
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Gupta S, Silveira DA, Mombach JCM. Modeling the role of microRNA-449a in the regulation of the G2/M cell cycle checkpoint in prostate LNCaP cells under ionizing radiation. PLoS One 2018; 13:e0200768. [PMID: 30024932 PMCID: PMC6053189 DOI: 10.1371/journal.pone.0200768] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/02/2018] [Indexed: 11/18/2022] Open
Abstract
Recent studies showed that induced microRNA-449a (miR-449a) enhances a G2/M cell cycle checkpoint arrest in prostate cancer (LNCaP) and lung adenocarcinoma cell lines. In the case of LNCaP cells, upregulated miR-449a directly downregulates c-Myc that is required to induce the cell cycle regulators Cdc25A and Cdc2/CyclinB whose inactivation blocks G2 to M phase transition. However, the molecular mechanisms involved are yet unclear, although in other prostate cancer cells the interactions among p53, miR-449a and Sirt-1 can affect the induction of the G2/M arrest. In order to clarify these molecular mechanisms, in this work we propose a boolean model of the G2/M checkpoint arrest regulation contemplating the influence of miR-449a. The model shows that the cell fate determination between two cellular phenotypes: G2/M-Arrest for DNA repair and G2/M-induced apoptosis is stochastic and influenced by miR-449a state of activation. The results were compared with experimental data available presenting agreement. We also found that several feedback loops are involved in this cell fate regulation and we indicate, through in silico gain or loss of function perturbations of genes, which of these feedback loops are more efficient to favor a specific phenotype.
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Affiliation(s)
- Shantanu Gupta
- Department of Physics, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Daner A. Silveira
- Department of Physics, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - José Carlos M. Mombach
- Department of Physics, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
- * E-mail:
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21
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Yuan GQ, Wei NL, Mu LY, Wang XQ, Zhang YN, Zhou WN, Pan YW. A 4-miRNAs signature predicts survival in glioblastoma multiforme patients. Cancer Biomark 2018; 20:443-452. [PMID: 28869437 DOI: 10.3233/cbm-170205] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Although O(6)-methylguanine DNA methyltransferase (MGMT) promoter methylation status is an important marker for glioblastoma multiforme (GBM), there is considerable variability in the clinical outcome of patients with similar methylation profles. OBJECTIVE We examined whether a MicroRNA (miRNA) signature can be identified for predicting clinical outcomes and helping in treatment decisions. METHODS The differentially expressed miRNAs were evaluated in 6 pairs of short- (⩽ 450 days) and long-term survivors (> 450 days) by using microarray. Real time quantitative PCR (qRT-PCR) was applied to further verify screened miRNAs with a greater number of samples (n= 48). Meanwhile, functional interpretation of miRNA profile was carried out based on miRNA-target databases. In addition, MGMT promoter methylation status was tested by means of pyrosequencing (PSQ) testing. RESULTS Six miRNAs were upregulated in the long-term survival group (fold change ⩾ 2.0, P< 0.05). The further verification by qRT-PCR indicated that the increase in let-7g-5p, miR-139-5p, miR-17-5p and miR-9-3p level in long-term survivors was statistically significant. Kaplan-Meier survival analysis showed that high expression of a prognostic 4-miRNA signature was significantly associated with good patient survival (p= 0.0012). The signature regulated signaling pathways including Calcium, MAPK, ErbB, mTOR and cell cycle involved in carcinogenesis from glial progenitor cell to primary GBM. CONCLUSIONS The 4-miRNA signature was identified as an independent prognostic biomarker that identified patients who have a favorable outcome.
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Affiliation(s)
- G Q Yuan
- Institute of Neurology, The Second Hospital, Lanzhou University, Lanzhou, Gansu 730030, China
| | - N L Wei
- Department of Neurosurgery, Fudan University Huashan Hospital, Fudan University, Shanghai 20040, China
| | - L Y Mu
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou, Gansu 730000, China
| | - X Q Wang
- Institute of Neurology, The Second Hospital, Lanzhou University, Lanzhou, Gansu 730030, China
| | - Y N Zhang
- Department of Neurosurgery, The Second Hospital, Lanzhou University, Lanzhou, Gansu 730030, China
| | - W N Zhou
- Department of Neurosurgery, The Second Hospital, Lanzhou University, Lanzhou, Gansu 730030, China
| | - Y W Pan
- Institute of Neurology, The Second Hospital, Lanzhou University, Lanzhou, Gansu 730030, China.,Department of Neurosurgery, The Second Hospital, Lanzhou University, Lanzhou, Gansu 730030, China
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22
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MicroRNA-17-92 is required for T-cell and B-cell pathogenicity in chronic graft-versus-host disease in mice. Blood 2018. [PMID: 29530952 DOI: 10.1182/blood-2017-06-789321] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chronic graft-versus-host disease (cGVHD) is characterized as autoimmune-like fibrosis and antibody production mediated by pathogenic T cells and B cells. MicroRNA-17-92 (miR-17-92) influences the survival, differentiation, and function of lymphocytes in cancer, infections, and autoimmunity. To determine whether miR-17-92 regulates T- and B-cell responses in cGVHD, we generated mice conditionally deficient for miR-17-92 in T cells, B cells, or both. Using murine models of allogeneic bone marrow transplantation, we demonstrate that expression of miR-17-92 in donor T and B cells is essential for the induction of both scleroderma and bronchiolitis obliterans in cGVHD. Mechanistically, miR-17-92 expressed in T cells not only enhances the differentiation of pathogenic T helper 1 (Th1) and Th17 cells, but also promotes the generation of follicular Th cells, germinal center (GC) B cells, and plasma cells. In B cells, miR-17-92 expression is required for autoantibody production and immunoglobulin G deposition in the skin. Furthermore, we evaluated a translational approach using antagomirs specific for either miR-17 or miR-19, key members in miR-17-92 cluster. In a lupus-like cGVHD model, systemic administration of anti-miR-17, but not anti-miR-19, alleviates clinical manifestations and proteinuria incidence in recipients through inhibiting donor lymphocyte expansion, B-cell activation, and GC responses. Blockade of miR-17 also ameliorates skin damage by reducing Th17 differentiation in a scleroderma-cGVHD model. Taken together, our work reveals that miR-17-92 is required for T-cell and B-cell differentiation and function, and thus for the development of cGVHD. Furthermore, pharmacological inhibition of miR-17 represents a potential therapeutic strategy for the prevention of cGVHD.
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23
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Sengupta D, Govindaraj V, Kar S. Alteration in microRNA-17-92 dynamics accounts for differential nature of cellular proliferation. FEBS Lett 2018; 592:446-458. [PMID: 29331028 DOI: 10.1002/1873-3468.12974] [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: 11/05/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
MicroRNAs associated with the mir-17-92 cluster are crucial regulators of the mammalian cell cycle, as they inhibit transcription factors related to the E2F family that tightly control decision-making events for a cell to commit for active cellular proliferation. Intriguingly, in many solid cancers, these mir-17-92 cluster members are overexpressed, whereas in some hematopoietic cancers they are down-regulated. Our proposed model of the Myc/E2F/mir-17-92 network demonstrates that the differential expression pattern of mir-17-92 in different cell types can be conceived due to having a contrasting E2F dynamics induced by mir-17-92. The model predicts that by explicitly altering the mir-17-92-related part of the network, experimentally it is possible to control cellular proliferation in a cell type-dependent manner for therapeutic intervention.
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Affiliation(s)
| | | | - Sandip Kar
- Department of Chemistry, IIT Bombay, Mumbai, India
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24
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Asiaf A, Ahmad ST, Arjumand W, Zargar MA. MicroRNAs in Breast Cancer: Diagnostic and Therapeutic Potential. Methods Mol Biol 2018; 1699:23-43. [PMID: 29086366 DOI: 10.1007/978-1-4939-7435-1_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a large family of small, approximately 20-22 nucleotide, noncoding RNAs that regulate the expression of target genes, at the post-transcriptional level. miRNAs are involved in virtually diverse biological processes and play crucial roles in cellular processes, such as cell differentiation, proliferation, and apoptosis. Accumulating lines of evidence have indicated that miRNAs play important roles in the maintenance of biological homeostasis and that aberrant expression levels of miRNAs are associated with the onset of many diseases, including cancer. It is possible that the diverse roles that miRNAs play, have potential to provide valuable information in a clinical setting, demonstrating the potential to act as both screening tools for the stratification of high-risk patients, while informing the treatment decision-making process. Increasing evidence suggests that some miRNAs may even provide assistance in the diagnosis of patients with breast cancer. In addition, miRNAs may themselves be considered therapeutic targets, with inhibition or reintroduction of a particular miRNA capable of inducing a response in-vivo. This chapter discusses the role of miRNAs as oncogenes and tumor suppressors in breast cancer development and metastasis . It focuses on miRNAs that have prognostic, diagnostic, or predictive potential in breast cancer as well as the possible challenges in the translation of such observations to the clinic.
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Affiliation(s)
- Asia Asiaf
- Department of Biochemistry, Faculty of Science, University of Kashmir, Hazratbal Srinagar, J&K, 190006, India
| | - Shiekh Tanveer Ahmad
- Clarke H. Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, 2A25 HRIC, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Wani Arjumand
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, 2A32 HRIC, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Mohammad Afzal Zargar
- Department of Biochemistry, Faculty of Science, University of Kashmir, Hazratbal Srinagar, J&K, 190006, India.
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Crosstalk between liver-related microRNAs and Wnt/β-catenin pathway in hepatocellular carcinoma patients. Arab J Gastroenterol 2017; 18:144-150. [PMID: 28958640 DOI: 10.1016/j.ajg.2017.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/07/2017] [Accepted: 09/04/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND STUDY AIMS Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide with highest incidence in Asia and Africa. MicroRNAs (miRNAs), a class of non-coding single stranded RNA, which not only post transcriptionally regulate gene expression but also respond to signaling molecules to affect cell functions such as Wnt/β-catenin signaling specifically in HCC. The goal of this study is to investigate the crosstalk between Wnt/β-catenin signaling proteins and microRNAs expression in HCC patients. PATIENTS AND METHODS Fresh tissue samples of 30 primary HCC patients and 10 control subjects were included. Expression level of 13 different miRNAs (miR-10a- miR-106b- miR-99a- miR-148a- miR-125b- miR-30e- miR-183- miR-155- miR-199a- miR-199a3p- miR-24- miR-122 and miR-215) were examined using real-time PCR assay. Five proteins involved in the Wnt/β-catenin pathway (β-catenin, APC, c-myc, survivin and cyclin D1) were analysed by immunohistochemistry technique. The correlation between miRNAs expression levels with protein expressions was assessed. RESULTS Up-regulation of miR-155 and miR-183 was reported in HCC patients compared to normal controls and this up-regulation was significantly correlated with liver cirrhosis in the case of miR-155 (p<0.05) referring to their oncogenic activity. Down-regulation was observed for 11 miRNAs in HCC indicating their tumour suppression activity. MiRNA-10a, miR-30e, miR-215, miR-125b and miR-148a were significantly correlated with the expression of important players in Wnt/β-catenin pathway including β-catenin, APC and c-myc (p<0.05). Detailed analysis revealed that miR-215 is associated with the grade of the disease and miR-125b is associated with HCV infection. CONCLUSION Collectively, our data showed potential role of miR-10a, miR-30e, miR-215, miR-125b and miR-148a as important mediators in HCC progression. Furthermore, their association with Wnt/β-catenin cascade proteins could be exploited to develop new therapeutic target strategies in HCC.
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26
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Audrito V, Serra S, Stingi A, Orso F, Gaudino F, Bologna C, Neri F, Garaffo G, Nassini R, Baroni G, Rulli E, Massi D, Oliviero S, Piva R, Taverna D, Mandalà M, Deaglio S. PD-L1 up-regulation in melanoma increases disease aggressiveness and is mediated through miR-17-5p. Oncotarget 2017; 8:15894-15911. [PMID: 28199980 PMCID: PMC5362532 DOI: 10.18632/oncotarget.15213] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/06/2017] [Indexed: 12/14/2022] Open
Abstract
PD-L1 is expressed by a subset of patients with metastatic melanoma (MM) with an unfavorable outcome. Its expression is increased in cells resistant to BRAF or MEK inhibitors (BRAFi or MEKi). However, the function and regulation of expression of PD-L1 remain incompletely understood. After generating BRAFi- and MEKi-resistant cell lines, we observed marked up-regulation of PD-L1 expression. These cells were characterized by a common gene expression profile with up-regulation of genes involved in cell movement. Consistently, in vitro they showed significantly increased invasive properties. This phenotype was controlled in part by PD-L1, as determined after silencing the molecule. Up-regulation of PD-L1 was due to post-transcriptional events controlled by miR-17-5p, which showed an inverse correlation with PD-L1 mRNA. Direct binding between miR-17-5p and the 3’-UTR of PD-L1 mRNA was demonstrated using luciferase reporter assays. In a cohort of 80 BRAF-mutated MM patients treated with BRAFi or MEKi, constitutive expression of PD-L1 in the absence of immune infiltrate, defined the patient subset with the worst prognosis. Furthermore, PD-L1 expression increased in tissue biopsies after the metastatic lesions became resistant to BRAFi or MEKi. Lastly, plasmatic miR-17-5p levels were higher in patients with PD-L1+ than PD-L1- lesions. In conclusion, our findings indicate that PD-L1 expression induces a more aggressive behavior in melanoma cells. We also show that PD-L1 up-regulation in BRAFi or MEKi-resistant cells is partly due to post-transcriptional mechanisms that involve miR-17-5p, suggesting that miR-17-5p may be used as a marker of PD-L1 expression by metastatic lesions and ultimately a predictor of responses to BRAFi or MEKi.
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Affiliation(s)
- Valentina Audrito
- Human Genetics Foundation (HuGeF), Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sara Serra
- Human Genetics Foundation (HuGeF), Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Aureliano Stingi
- Human Genetics Foundation (HuGeF), Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Francesca Orso
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federica Gaudino
- Human Genetics Foundation (HuGeF), Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Cinzia Bologna
- Human Genetics Foundation (HuGeF), Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Giulia Garaffo
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Romina Nassini
- Department of Health Sciences, University of Florence, Italy
| | - Gianna Baroni
- Department of Surgery and Translational Medicine, University of Florence, Italy
| | - Eliana Rulli
- Methodology for Clinical Research Laboratory, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Daniela Massi
- Department of Surgery and Translational Medicine, University of Florence, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), Turin, Italy.,Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Roberto Piva
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Daniela Taverna
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Mario Mandalà
- Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Silvia Deaglio
- Human Genetics Foundation (HuGeF), Turin, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
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27
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Johnson EL, Robinson DG, Coller HA. Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence. BMC Genomics 2017; 18:123. [PMID: 28143407 PMCID: PMC5286691 DOI: 10.1186/s12864-017-3521-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/26/2017] [Indexed: 01/29/2023] Open
Abstract
Background Quiescence, reversible exit from the cell division cycle, is characterized by large-scale changes in steady-state gene expression, yet mechanisms controlling these changes are in need of further elucidation. In order to characterize the effects of post-transcriptional control on the quiescent transcriptome in human fibroblasts, we determined mRNA decay rates for over 10,000 genes using a transcription shut-off time-course. Results We found that ~500 of the genes monitored exhibited significant changes in decay rate upon quiescence induction. Genes involved in RNA processing and ribosome biogenesis were destabilized with quiescence, while genes involved in the developmental process were stabilized with quiescence. Moreover, extracellular matrix genes demonstrated an upregulation of gene expression that corresponded with a stabilization of these transcripts. Additionally, targets of a quiescence-associated microRNA (miR-29) were significantly enriched in the fraction of transcripts that were stabilized during quiescence. Conclusion Coordinated stability changes in clusters of genes with important functions in fibroblast quiescence maintenance are highly correlated with quiescence gene expression patterns. Analysis of miR-29 target decay rates suggests that microRNA-induced changes in RNA stability are important contributors to the quiescence gene expression program in fibroblasts. The identification of multiple stability-related gene clusters suggests that other posttranscriptional regulators of transcript stability may contribute to the coordination of quiescence gene expression. Such regulators may ultimately prove to be valuable targets for therapeutics that target proliferative cells, for instance, in cancer or fibrosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3521-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth L Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - David G Robinson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, David Geffen School of Medicine, Los Angeles, CA, 90095, USA.
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28
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Wang F, Meng F, Wang L. Co-expression Pattern Analysis of miR-17-92 Target Genes in Chronic Myelogenous Leukemia. Front Genet 2016; 7:167. [PMID: 27708666 PMCID: PMC5030476 DOI: 10.3389/fgene.2016.00167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/05/2016] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that regulate gene expression by binding to the 3' untranslated region of target mRNAs. Mature miRNAs transcribed from the miR-17-92 cluster have an oncogenic activity, which are overexpressed in chronic-phase chronic myelogenous leukemia (CML) patients compared with normal individuals. Besides, the tyrosine kinase activity of BCR-ABL oncoprotein from the Philadelphia chromosome in CML can affect this miRNA cluster. Genes with similar mRNA expression profiles are likely to be regulated by the same regulators. We hypothesize that target genes regulated by the same miRNA are co-expressed. In this study, we aim to explore the difference in the co-expression patterns of those genes potentially regulated by miR-17-92 cluster between the normal and the CML groups. We applied a statistical method for gene pair classification by identifying a disease-specific cutoff point that classified the co-expressed gene pairs into strong and weak co-expression classes. The method effectively identified the differences in the co-expression patterns from the overall structure. Functional annotation for co-expressed gene pairs showed that genes involved in the metabolism processes were more likely to be co-expressed in the normal group compared to the CML group. Our method can identify the co-expression pattern difference from the overall structure between two different distributions using the distribution-based statistical method. Functional annotation further provides the biological support. The co-expression pattern in the normal group is regarded as the inter-gene linkages, which represents the healthy pathological balance. Dysregulation of metabolism may be related to CML pathology. Our findings will provide useful information for investigating the novel CML mechanism and treatment.
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Affiliation(s)
- Fengfeng Wang
- Department of Health Technology and Informatics, Hong Kong Polytechnic UniversityHong Kong, China
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29
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Ueki S, Murakami Y, Yamada S, Kimura M, Saito Y, Saito H. microRNA-mediated resistance to hypoglycemia in the HepG2 human hepatoma cell line. BMC Cancer 2016; 16:732. [PMID: 27629773 PMCID: PMC5024426 DOI: 10.1186/s12885-016-2762-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/06/2016] [Indexed: 12/20/2022] Open
Abstract
Background It is generally accepted that the energy resources of cancer cells rely on anaerobic metabolism or the glycolytic system, even if they have sufficient oxygen. This is known as the Warburg effect. The cells skillfully survive under hypoglycemic conditions when their circumstances change, which probably at least partly involves microRNA (miRNA)-mediated regulation. Methods To determine how cancer cells exploit miRNA-mediated epigenetic mechanisms to survive in hypoglycemic conditions, we used DNA microarray analysis to comprehensively and simultaneously compare the expression of miRNAs and mRNAs in the HepG2 human hepatoma cell line and in cultured normal human hepatocytes. Results The hypoglycemic condition decreased the expression of miRNA-17-5p and -20a-5p in hepatoma cells and consequently upregulated the expression of their target gene p21. These regulations were also confirmed by using antisense inhibitors of these miRNAs. In addition to this change, the hypoglycemic condition led to upregulated expression of heat shock proteins and increased resistance to caspase-3-induced apoptosis. However, we could not identify miRNA-mediated regulations, despite using comprehensive detection. Several interesting genes were also found to be upregulated in the hypoglycemic condition by the microarray analysis, probably because of responding to this cellular stress. Conclusion These results suggest that cancer cells skillfully survive in hypoglycemic conditions, which frequently occur in malignancies, and that some of the gene regulation of this process is manipulated by miRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2762-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Satomi Ueki
- Department of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, 1058512, Japan
| | - Yuko Murakami
- Department of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, 1058512, Japan
| | - Shoji Yamada
- Department of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, 1058512, Japan
| | - Masaki Kimura
- Department of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, 1058512, Japan
| | - Yoshimasa Saito
- Department of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, 1058512, Japan
| | - Hidetsugu Saito
- Department of Pharmacotherapeutics, Faculty of Pharmacy, Keio University, Minato-ku, Tokyo, 1058512, Japan.
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30
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Genomic imbalances and microRNA transcriptional profiles in patients with mycosis fungoides. Tumour Biol 2016; 37:13637-13647. [DOI: 10.1007/s13277-016-5259-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/15/2016] [Indexed: 01/12/2023] Open
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31
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Zhang F, Cheng D, Wang S, Zhu J. Human Specific Regulation of the Telomerase Reverse Transcriptase Gene. Genes (Basel) 2016; 7:genes7070030. [PMID: 27367732 PMCID: PMC4962000 DOI: 10.3390/genes7070030] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 12/19/2022] Open
Abstract
Telomerase, regulated primarily by the transcription of its catalytic subunit telomerase reverse transcriptase (TERT), is critical for controlling cell proliferation and tissue homeostasis by maintaining telomere length. Although there is a high conservation between human and mouse TERT genes, the regulation of their transcription is significantly different in these two species. Whereas mTERT expression is widely detected in adult mice, hTERT is expressed at extremely low levels in most adult human tissues and cells. As a result, mice do not exhibit telomere-mediated replicative aging, but telomere shortening is a critical factor of human aging and its stabilization is essential for cancer development in humans. The chromatin environment and epigenetic modifications of the hTERT locus, the binding of transcriptional factors to its promoter, and recruitment of nucleosome modifying complexes all play essential roles in restricting its transcription in different cell types. In this review, we will discuss recent progress in understanding the molecular mechanisms of TERT regulation in human and mouse tissues and cells, and during cancer development.
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Affiliation(s)
- Fan Zhang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
| | - De Cheng
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
| | - Shuwen Wang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
| | - Jiyue Zhu
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, PO Box 1495, Spokane, WA 99210, USA.
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32
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Dal Bo M, Bomben R, Hernández L, Gattei V. The MYC/miR-17-92 axis in lymphoproliferative disorders: A common pathway with therapeutic potential. Oncotarget 2016; 6:19381-92. [PMID: 26305986 PMCID: PMC4637292 DOI: 10.18632/oncotarget.4574] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/10/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) represent a class of small non-coding single-stranded RNA molecules acting as master regulators of gene expression post transcriptionally by inhibiting the translation or inducing the degradation of target messenger RNAs (mRNAs). In particular, the miR-17-92 cluster is widely expressed in many different cell types and is essential for many developmental and pathogenic processes. As a strong oncogene, miR-17-92 can regulate multiple cellular processes that favor malignant transformation, promoting cell survival, rapid cell proliferation, and increased angiogenesis. The miR-17-92 cluster has been reported to be involved in hematopoietic malignancies including diffuse large B-cell lymphoma, mantle cell lymphoma, Burkitt's lymphoma, and chronic lymphocytic leukemia. Given the multiple and potent effects on cellular proliferation and apoptosis exerted by the miR-17-92 cluster, miRNAs belonging to the cluster surely represent attractive targets for cancer therapy also in the context of lymphoproliferative disorders. In the present review, we focus on the role of the miR-17-92 cluster in lymphoproliferative disorders, including diagnostic/prognostic implications, and on the potential applications of anti-miRNAs based therapies targeting miRNAs belonging to the cluster.
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Affiliation(s)
- Michele Dal Bo
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., Aviano PN, Italy
| | - Riccardo Bomben
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., Aviano PN, Italy
| | - Luis Hernández
- Department of Pathology, Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Valter Gattei
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., Aviano PN, Italy
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Roisman A, Huamán Garaicoa F, Metrebian F, Narbaitz M, Kohan D, García Rivello H, Fernandez I, Pavlovsky A, Pavlovsky M, Hernández L, Slavutsky I. SOXC and MiR17-92 gene expression profiling defines two subgroups with different clinical outcome in mantle cell lymphoma. Genes Chromosomes Cancer 2016; 55:531-40. [PMID: 26998831 DOI: 10.1002/gcc.22355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 12/12/2022] Open
Abstract
Mantle cell lymphoma (MCL) is a heterogeneous B-cell lymphoid malignancy where most patients follow an aggressive clinical course whereas others are associated with an indolent performance. SOX4, SOX11, and SOX12 belong to SOXC family of transcription factors involved in embryonic neurogenesis and tissue remodeling. Among them, SOX11 has been found aberrantly expressed in most aggressive MCL patients, being considered a reliable biomarker in the pathology. Several studies have revealed that microRNAs (miRs) from the miR-17-92 cluster are among the most deregulated miRNAs in human cancers, still little is known about this cluster in MCL. In this study we screened the transcriptional profiles of 70 MCL patients for SOXC cluster and miR17, miR18a, miR19b and miR92a, from the miR-17-92 cluster. Gene expression analysis showed higher SOX11 and SOX12 levels compared to SOX4 (P ≤ 0.0026). Moreover we found a negative correlation between the expression of SOX11 and SOX4 (P < 0.0001). miR17-92 cluster analysis showed that miR19b and miR92a exhibited higher levels than miR17 and miR18a (P < 0.0001). Unsupervised hierarchical clustering revealed two subgroups with significant differences in relation to aggressive MCL features, such as blastoid morphological variant (P = 0.0412), nodal presentation (P = 0.0492), CD5(+) (P = 0.0004) and shorter overall survival (P < 0.0001). Together, our findings show for the first time an association between the differential expression profiles of SOXC and miR17-92 clusters in MCL and also relate them to different clinical subtypes of the disease adding new biological information that may contribute to a better understanding of this pathology. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alejandro Roisman
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina (ANM), Buenos Aires, Argentina
| | - Fuad Huamán Garaicoa
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina (ANM), Buenos Aires, Argentina.,FUNDALEU, Buenos Aires, Argentina
| | - Fernanda Metrebian
- División Patología, Instituto de Investigaciones Hematológicas, ANM, Buenos Aires, Argentina
| | - Marina Narbaitz
- FUNDALEU, Buenos Aires, Argentina.,División Patología, Instituto de Investigaciones Hematológicas, ANM, Buenos Aires, Argentina
| | - Dana Kohan
- Servicio de Patología, Hospital Italiano, Buenos Aires, Argentina
| | | | | | | | | | - Luis Hernández
- Patología Molecular, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, España
| | - Irma Slavutsky
- Laboratorio de Genética de Neoplasias Linfoides, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina (ANM), Buenos Aires, Argentina
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Peng Y, Croce CM. The role of MicroRNAs in human cancer. Signal Transduct Target Ther 2016; 1:15004. [PMID: 29263891 PMCID: PMC5661652 DOI: 10.1038/sigtrans.2015.4] [Citation(s) in RCA: 1489] [Impact Index Per Article: 186.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 11/25/2015] [Accepted: 11/29/2015] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous, small non-coding RNAs that function in regulation of gene expression. Compelling evidences have demonstrated that miRNA expression is dysregulated in human cancer through various mechanisms, including amplification or deletion of miRNA genes, abnormal transcriptional control of miRNAs, dysregulated epigenetic changes and defects in the miRNA biogenesis machinery. MiRNAs may function as either oncogenes or tumor suppressors under certain conditions. The dysregulated miRNAs have been shown to affect the hallmarks of cancer, including sustaining proliferative signaling, evading growth suppressors, resisting cell death, activating invasion and metastasis, and inducing angiogenesis. An increasing number of studies have identified miRNAs as potential biomarkers for human cancer diagnosis, prognosis and therapeutic targets or tools, which needs further investigation and validation. In this review, we focus on how miRNAs regulate the development of human tumors by acting as tumor suppressors or oncogenes.
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Affiliation(s)
- Yong Peng
- Department of Thoracic Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Carlo M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
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Cioffi M, Trabulo SM, Sanchez-Ripoll Y, Miranda-Lorenzo I, Lonardo E, Dorado J, Reis Vieira C, Ramirez JC, Hidalgo M, Aicher A, Hahn S, Sainz B, Heeschen C. The miR-17-92 cluster counteracts quiescence and chemoresistance in a distinct subpopulation of pancreatic cancer stem cells. Gut 2015; 64:1936-48. [PMID: 25887381 PMCID: PMC4680182 DOI: 10.1136/gutjnl-2014-308470] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/04/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Cancer stem cells (CSCs) represent the root of many solid cancers including pancreatic ductal adenocarcinoma, are highly chemoresistant and represent the cellular source for disease relapse. However the mechanisms involved in these processes still need to be fully elucidated. Understanding the mechanisms implicated in chemoresistance and metastasis of pancreatic cancer is critical to improving patient outcomes. DESIGN Micro-RNA (miRNA) expression analyses were performed to identify functionally defining epigenetic signatures in pancreatic CSC-enriched sphere-derived cells and gemcitabine-resistant pancreatic CSCs. RESULTS We found the miR-17-92 cluster to be downregulated in chemoresistant CSCs versus non-CSCs and demonstrate its crucial relevance for CSC biology. In particular, overexpression of miR-17-92 reduced CSC self-renewal capacity, in vivo tumourigenicity and chemoresistance by targeting multiple NODAL/ACTIVIN/TGF-β1 signalling cascade members as well as directly inhibiting the downstream targets p21, p57 and TBX3. Overexpression of miR-17-92 translated into increased CSC proliferation and their eventual exhaustion via downregulation of p21 and p57. Finally, the translational impact of our findings could be confirmed in preclinical models for pancreatic cancer. CONCLUSIONS Our findings therefore identify the miR-17-92 cluster as a functionally determining family of miRNAs in CSCs, and highlight the putative potential of developing modulators of this cluster to overcome drug resistance in pancreatic CSCs.
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Affiliation(s)
| | | | | | | | | | | | - Catarina Reis Vieira
- Stem Cells & Cancer Group, CNIO, Madrid, Spain,Viral Vector Unit, Spanish National Cardiovascular Research Centre (CNIC), Madrid, Spain
| | - Juan Carlos Ramirez
- Viral Vector Unit, Spanish National Cardiovascular Research Centre (CNIC), Madrid, Spain
| | - Manuel Hidalgo
- Gastrointestinal Cancer Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Stephan Hahn
- Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Bruno Sainz
- Stem Cells & Cancer Group, CNIO, Madrid, Spain
| | - Christopher Heeschen
- Stem Cells & Cancer Group, CNIO, Madrid, Spain,Barts Cancer Institute, Centre for Stem Cells in Cancer & Ageing, Queen Mary University of London, London, UK
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Mihailovich M, Bremang M, Spadotto V, Musiani D, Vitale E, Varano G, Zambelli F, Mancuso FM, Cairns DA, Pavesi G, Casola S, Bonaldi T. miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nat Commun 2015; 6:8725. [PMID: 26555894 PMCID: PMC4667639 DOI: 10.1038/ncomms9725] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/22/2015] [Indexed: 01/07/2023] Open
Abstract
The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 3′ untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c-MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 3′ UTR shortening at different stages of tumorigenesis. The synergism between c-MYC and miR-17-19b plays an important role in lymphoma initiation. In this study, the authors identify a panel of targets co-regulated by miR-17-19b and in MYC-driven lymphoma and unravel the molecular mechanism through which miR-17-19b inhibits MYC translation.
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Affiliation(s)
- Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Valeria Spadotto
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Daniele Musiani
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Elena Vitale
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Gabriele Varano
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | | | - Francesco M Mancuso
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - David A Cairns
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Giulio Pavesi
- Department of Biosciences, Milan University, Milan 20133, Italy
| | - Stefano Casola
- Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
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Jackstadt R, Hermeking H. MicroRNAs as regulators and mediators of c-MYC function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:544-53. [DOI: 10.1016/j.bbagrm.2014.04.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/27/2014] [Accepted: 04/04/2014] [Indexed: 12/19/2022]
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Mognato M, Celotti L. MicroRNAs Used in Combination with Anti-Cancer Treatments Can Enhance Therapy Efficacy. Mini Rev Med Chem 2015; 15:1052-62. [PMID: 26156420 PMCID: PMC4997954 DOI: 10.2174/1389557515666150709115355] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 06/23/2015] [Accepted: 07/08/2015] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs), a recently discovered class of small non-coding RNAs, constitute a promising approach to anti-cancer treatments when they are used in combination with other agents. MiRNAs are evolutionarily conserved non-coding RNAs that negatively regulate gene expression by binding to the complementary sequence in the 3'-untranslated region (UTR) of target genes. MiRNAs typically suppress gene expression by direct association with target transcripts, thus decreasing the expression levels of target proteins. The delivery to cells of synthetic miRNAs that mimic endogenous miRNA targeting genes involved in the DNA-Damage Response (DDR) can perturb the process, making cells more sensitive to chemotherapy or radiotherapy. This review examines how cells respond to combined therapy and it provides insights into the role of miRNAs in targeting the DDR repair pathway when they are used in combination with chemical compounds or ionizing radiation to enhance cellular sensitivity to treatments.
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Affiliation(s)
- Maddalena Mognato
- Department of Biology, School of Science, University of Padova, Padova, Italy.
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Abstract
Malignant neoplasms are consistently among the top four leading causes of death in all age groups in the United States, despite a concerted effort toward developing novel therapeutic approaches. Our understanding of and therapeutic strategy for treating each of these neoplastic diseases have been improved through decades of research on the genetics, signaling pathways, and cellular biology that govern tumor cell initiation, progression and maintenance. Much of this work has concentrated on post-translational modifications and abnormalities at the DNA level, including point mutations, amplifications/deletions, and chromosomal translocations, and how these aberrant events affect the expression and function of protein-coding genes. Only recently has a novel class of conserved gene regulatory molecules been identified as a major contributor to malignant neoplastic disease. This review focuses on how these small non-coding RNA molecules, termed microRNAs (miRNAs), can function as oncogenes or tumor suppressors, and how the misexpression of miRNAs and dysregulation of factors that regulate miRNAs contribute to the tumorigenic process. Specific focus is given to more recently discovered regulatory mechanisms that go awry in cancer, and how these changes alter miRNA expression, processing, and function.
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Affiliation(s)
- Brian D Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Andrea L Kasinski
- Department of Biological Sciences, Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
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Novel approach for coexpression analysis of E2F1-3 and MYC target genes in chronic myelogenous leukemia. BIOMED RESEARCH INTERNATIONAL 2014; 2014:439840. [PMID: 25180182 PMCID: PMC4142389 DOI: 10.1155/2014/439840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/23/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND Chronic myelogenous leukemia (CML) is characterized by tremendous amount of immature myeloid cells in the blood circulation. E2F1-3 and MYC are important transcription factors that form positive feedback loops by reciprocal regulation in their own transcription processes. Since genes regulated by E2F1-3 or MYC are related to cell proliferation and apoptosis, we wonder if there exists difference in the coexpression patterns of genes regulated concurrently by E2F1-3 and MYC between the normal and the CML states. RESULTS We proposed a method to explore the difference in the coexpression patterns of those candidate target genes between the normal and the CML groups. A disease-specific cutoff point for coexpression levels that classified the coexpressed gene pairs into strong and weak coexpression classes was identified. Our developed method effectively identified the coexpression pattern differences from the overall structure. Moreover, we found that genes related to the cell adhesion and angiogenesis properties were more likely to be coexpressed in the normal group when compared to the CML group. CONCLUSION Our findings may be helpful in exploring the underlying mechanisms of CML and provide useful information in cancer treatment.
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Zhang Y, Zhang A, Shen C, Zhang B, Rao Z, Wang R, Yang S, Ning S, Mao G, Fang D. E2F1 acts as a negative feedback regulator of c-Myc‑induced hTERT transcription during tumorigenesis. Oncol Rep 2014; 32:1273-80. [PMID: 24969314 DOI: 10.3892/or.2014.3287] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/03/2014] [Indexed: 11/05/2022] Open
Abstract
Since induction of hTERT expression and subsequent telomerase activation play a critical role in the multistep process of tumorigenesis, a better understanding of hTERT regulation may provide not only a rationale for the molecular basis of cancer progression but also a path to the development of cancer prevention. The c-Myc oncoprotein can function effectively in activating the transcriptional expression of hTERT through E-box elements on its promoter. E2F transcription factor 1 (E2F1) was found to be a repressor of hTERT transcription by directly binding to its promoter, thereby inhibiting hTERT protein expression. For the extensively crosstalk between c-Myc and E2F1 signals, which is now known to be vital to cell fate, we speculated that E2F1 may play a negative regulatory role in c-Myc-induced hTERT transcription. In the present study, we chose to use human embryonic fibroblast cells as an experimental model system, and present evidence that the E2F1 transcription factor constitutes a negative regulatory system to limit c-Myc transcriptional activation of hTERT in normal cells. Furthermore, we demonstrated that upregulation of the miR-17-92 cluster (miR-20a/miR-17-5p) is involved in the regulation of E2F1-mediated negative feedback of the c-Myc/hTERT pathway. Our results not only reveal novel insights into how normal cells control the transmission of c-Myc-mediated oncogenic signals, but also further establish E2F1 as an important molecular target for cancer therapy.
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Affiliation(s)
- Yafei Zhang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P.R. China
| | - Anran Zhang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P.R. China
| | - Caifei Shen
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P.R. China
| | - Bicheng Zhang
- Department of Oncology, Wuhan General Hospital of Guangzhou Command, People's Liberation Army, Wuhan, P.R. China
| | - Zhiguo Rao
- Department of Oncology, Wuhan General Hospital of Guangzhou Command, People's Liberation Army, Wuhan, P.R. China
| | - Rongquan Wang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P.R. China
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, P.R. China
| | - Shoubin Ning
- Department of Gastroenterology, Air Force General Hospital of Chinese PLA, Beijing, P.R. China
| | - Gaoping Mao
- Department of Gastroenterology, Air Force General Hospital of Chinese PLA, Beijing, P.R. China
| | - Dianchun Fang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P.R. China
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Guglielmi L, Cinnella C, Nardella M, Maresca G, Valentini A, Mercanti D, Felsani A, D'Agnano I. MYCN gene expression is required for the onset of the differentiation programme in neuroblastoma cells. Cell Death Dis 2014; 5:e1081. [PMID: 24556696 PMCID: PMC3944258 DOI: 10.1038/cddis.2014.42] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 02/08/2023]
Abstract
Neuroblastoma is an embryonic tumour of the sympathetic nervous system and is one of the most common cancers in childhood. A high differentiation stage has been associated with a favourable outcome; however, the mechanisms governing neuroblastoma cell differentiation are not completely understood. The MYCN gene is considered the hallmark of neuroblastoma. Even though it has been reported that MYCN has a role during embryonic development, it is needed its decrease so that differentiation can be completed. We aimed to better define the role of MYCN in the differentiation processes, particularly during the early stages. Considering the ability of MYCN to regulate non-coding RNAs, our hypothesis was that N-Myc protein might be necessary to activate differentiation (mimicking embryonic development events) by regulating miRNAs critical for this process. We show that MYCN expression increased in embryonic cortical neural precursor cells at an early stage after differentiation induction. To investigate our hypothesis, we used human neuroblastoma cell lines. In LAN-5 neuroblastoma cells, MYCN was upregulated after 2 days of differentiation induction before its expected downregulation. Positive modulation of various differentiation markers was associated with the increased MYCN expression. Similarly, MYCN silencing inhibited such differentiation, leading to negative modulation of various differentiation markers. Furthermore, MYCN gene overexpression in the poorly differentiating neuroblastoma cell line SK-N-AS restored the ability of such cells to differentiate. We identified three key miRNAs, which could regulate the onset of differentiation programme in the neuroblastoma cells in which we modulated MYCN. Interestingly, these effects were accompanied by changes in the apoptotic compartment evaluated both as expression of apoptosis-related genes and as fraction of apoptotic cells. Therefore, our idea is that MYCN is necessary during the activation of neuroblastoma differentiation to induce apoptosis in cells that are not committed to differentiate.
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Affiliation(s)
- L Guglielmi
- CNR, Institute of Cell Biology and Neurobiology, Rome, Italy
| | - C Cinnella
- CNR, Institute of Cell Biology and Neurobiology, Rome, Italy
| | - M Nardella
- CNR, Institute of Cell Biology and Neurobiology, Rome, Italy
| | - G Maresca
- CNR, Institute of Cell Biology and Neurobiology, Rome, Italy
| | - A Valentini
- PTV, Laboratory Medicine and Internal Medicine Departments, University of Rome 'Tor Vergata', Rome, Italy
| | - D Mercanti
- CNR, Institute of Cell Biology and Neurobiology, Rome, Italy
| | - A Felsani
- CNR, Institute of Cell Biology and Neurobiology, Rome, Italy
| | - I D'Agnano
- CNR, Institute of Cell Biology and Neurobiology, Rome, Italy
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43
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Small silencing non-coding RNAs: cancer connections and significance. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Fuentes TI, Appleby N, Tsay E, Martinez JJ, Bailey L, Hasaniya N, Kearns-Jonker M. Human neonatal cardiovascular progenitors: unlocking the secret to regenerative ability. PLoS One 2013; 8:e77464. [PMID: 24204836 PMCID: PMC3810469 DOI: 10.1371/journal.pone.0077464] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/03/2013] [Indexed: 01/07/2023] Open
Abstract
Although clinical benefit can be achieved after cardiac transplantation of adult c-kit+ or cardiosphere-derived cells for myocardial repair, these stem cells lack the regenerative capacity unique to neonatal cardiovascular stem cells. Unraveling the molecular basis for this age-related discrepancy in function could potentially transform cardiovascular stem cell transplantation. In this report, clonal populations of human neonatal and adult cardiovascular progenitor cells were isolated and characterized, revealing the existence of a novel subpopulation of endogenous cardiovascular stem cells that persist throughout life and co-express both c-kit and isl1. Epigenetic profiling identified 41 microRNAs whose expression was significantly altered with age in phenotypically-matched clones. These differences were correlated with reduced proliferation and a limited capacity to invade in response to growth factor stimulation, despite high levels of growth factor receptor on progenitors isolated from adults. Further understanding of these differences may provide novel therapeutic targets to enhance cardiovascular regenerative capacity.
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Affiliation(s)
- Tania I. Fuentes
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, California, United States of America
| | - Nancy Appleby
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, California, United States of America
| | - Eric Tsay
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, California, United States of America
| | - J. Julian Martinez
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, California, United States of America
| | - Leonard Bailey
- Department of Cardiothoracic Surgery, Loma Linda University School of Medicine, Loma Linda, California, United States of America
| | - Nahidh Hasaniya
- Department of Cardiothoracic Surgery, Loma Linda University School of Medicine, Loma Linda, California, United States of America
| | - Mary Kearns-Jonker
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, California, United States of America
- * E-mail:
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45
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El Tayebi HM, Omar K, Hegy S, El Maghrabi M, El Brolosy M, Hosny KA, Esmat G, Abdelaziz AI. Repression of miR-17-5p with elevated expression of E2F-1 and c-MYC in non-metastatic hepatocellular carcinoma and enhancement of cell growth upon reversing this expression pattern. Biochem Biophys Res Commun 2013; 434:421-7. [PMID: 23583198 DOI: 10.1016/j.bbrc.2013.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 12/12/2022]
Abstract
E2F-1, c-MYC, and miR-17-5p is a triad of two regulatory loops: a negative and a positive loop, where c-MYC induces the expression of E2F-1 that induces the expression of miR-17-5p which in turn reverses the expression of E2F-1 to close the loop. In this study, we investigated this triad for the first time in hepatocellular carcinoma (HCC), where miR-17-5p showed a significant down-regulation in 23 non-metastatic HCC biopsies compared to 10 healthy tissues; however, E2F-1 and c-MYC transcripts were markedly elevated. Forced over-expression of miR-17-5p in HuH-7 cells resulted in enhanced cell proliferation, growth, migration and clonogenicity with concomitant inhibition of E2F-1 and c-MYC transcripts expressions, while antagomirs of miR-17-5p reversed these events. In conclusion, this study revealed a unique pattern of expression for miR-17-5p in non-metastatic HCC patients in contrast to metastatic HCC patients. In addition we show that miR-17-5p is the key player among the triad that tumor growth and spread.
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Affiliation(s)
- H M El Tayebi
- The Molecular Pathology Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
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Yang L, Meng Y, Bao C, Liu W, Ma C, Li A, Xuan Z, Shan G, Jia Y. Robustness and backbone motif of a cancer network regulated by miR-17-92 cluster during the G1/S transition. PLoS One 2013; 8:e57009. [PMID: 23469179 PMCID: PMC3585929 DOI: 10.1371/journal.pone.0057009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/16/2013] [Indexed: 11/18/2022] Open
Abstract
Based on interactions among transcription factors, oncogenes, tumor suppressors and microRNAs, a Boolean model of cancer network regulated by miR-17-92 cluster is constructed, and the network is associated with the control of G1/S transition in the mammalian cell cycle. The robustness properties of this regulatory network are investigated by virtue of the Boolean network theory. It is found that, during G1/S transition in the cell cycle process, the regulatory networks are robustly constructed, and the robustness property is largely preserved with respect to small perturbations to the network. By using the unique process-based approach, the structure of this network is analyzed. It is shown that the network can be decomposed into a backbone motif which provides the main biological functions, and a remaining motif which makes the regulatory system more stable. The critical role of miR-17-92 in suppressing the G1/S cell cycle checkpoint and increasing the uncontrolled proliferation of the cancer cells by targeting a genetic network of interacting proteins is displayed with our model.
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Affiliation(s)
- Lijian Yang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Yan Meng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Chun Bao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wangheng Liu
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Chengzhang Ma
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Anbang Li
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Zhan Xuan
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
| | - Ge Shan
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- * E-mail: (YJ); (GS)
| | - Ya Jia
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China
- * E-mail: (YJ); (GS)
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47
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Suh EJ, Remillard MY, Legesse-Miller A, Johnson EL, Lemons JMS, Chapman TR, Forman JJ, Kojima M, Silberman ES, Coller HA. A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts. Genome Biol 2012; 13:R121. [PMID: 23259597 PMCID: PMC3924601 DOI: 10.1186/gb-2012-13-12-r121] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/22/2012] [Indexed: 01/01/2023] Open
Abstract
Background Although quiescence (reversible cell cycle arrest) is a key part in the life history and fate of many mammalian cell types, the mechanisms of gene regulation in quiescent cells are poorly understood. We sought to clarify the role of microRNAs as regulators of the cellular functions of quiescent human fibroblasts. Results Using microarrays, we discovered that the expression of the majority of profiled microRNAs differed between proliferating and quiescent fibroblasts. Fibroblasts induced into quiescence by contact inhibition or serum starvation had similar microRNA profiles, indicating common changes induced by distinct quiescence signals. By analyzing the gene expression patterns of microRNA target genes with quiescence, we discovered a strong regulatory function for miR-29, which is downregulated with quiescence. Using microarrays and immunoblotting, we confirmed that miR-29 targets genes encoding collagen and other extracellular matrix proteins and that those target genes are induced in quiescence. In addition, overexpression of miR-29 resulted in more rapid cell cycle re-entry from quiescence. We also found that let-7 and miR-125 were upregulated in quiescent cells. Overexpression of either one alone resulted in slower cell cycle re-entry from quiescence, while the combination of both together slowed cell cycle re-entry even further. Conclusions microRNAs regulate key aspects of fibroblast quiescence including the proliferative state of the cells as well as their gene expression profiles, in particular, the induction of extracellular matrix proteins in quiescent fibroblasts.
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48
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Parpart S, Wang XW. microRNA Regulation and Its Consequences in Cancer. CURRENT PATHOBIOLOGY REPORTS 2012; 1:71-79. [PMID: 23420713 DOI: 10.1007/s40139-012-0002-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNA (miRNA) function has been studied extensively in the last two decades. These short, non-coding RNAs influence a variety of cellular processes through repression of target genes. With the number of genes that a single miRNA can target, the biological effects of one miRNA alone can be vast. In cancer, aberrant miRNA expression is ubiquitous and consequently it can provoke progression of the disease. Though much is known about the downstream effects of miRNA, the mechanisms that control the level of miRNA expression itself are not well documented. In this review, we will focus on how miRNAs are regulated as well as potential therapeutic targets that can be exploited for cancer therapy.
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Affiliation(s)
- Sonya Parpart
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 ; Department of Oncology, Lombardi Cancer Center, Georgetown University, Washington, DC 20057
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Chen PS, Su JL, Hung MC. Dysregulation of microRNAs in cancer. J Biomed Sci 2012; 19:90. [PMID: 23075324 PMCID: PMC3482395 DOI: 10.1186/1423-0127-19-90] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 10/16/2012] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in multiple biological activities as well as disease progression including cancer. Interestingly, miRNAs could act as either tumor suppressors or oncogenes depending on the functions of their targets. Using high-throughput profiling, dysregulation of miRNAs has been widely observed in different stages of cancer, and there is mounting evidence demonstrating several misguided mechanisms that cause miRNA dysregulation. In this review, we summarize the key functions of miRNAs in cancer, especially those affecting tumor metastasis and drug resistance. Moreover, the mechanisms leading to dysregulation of miRNAs, including genomic abnormalities, DNA/histone modifications, transcriptional regulation, abnormal biogenesis, and interaction between miRNAs, are also discussed.
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Affiliation(s)
- Pai-Sheng Chen
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
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50
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Davis-Dusenbery BN, Hata A. MicroRNA in Cancer: The Involvement of Aberrant MicroRNA Biogenesis Regulatory Pathways. Genes Cancer 2012; 1:1100-14. [PMID: 21533017 DOI: 10.1177/1947601910396213] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that influence diverse biological outcomes through the repression of target genes during normal development and pathological responses. In particular, the alteration of miRNA expression has dramatic consequences for the progression of tumorigenesis. miRNAs undergo two processing steps that transform a long primary transcript into the mature miRNA. Although the general miRNA biogenesis pathway is well established, it is clear that not all miRNAs are created equally. Recent studies show that miRNA expression is controlled by diverse mechanisms in response to cellular stimuli. In this review, we discuss the mechanisms that govern the regulation of miRNA biogenesis with particular focus on how these mechanisms are perturbed in cancer.
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