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Mohapatra S, Banerjee A, Rausseo P, Dragomir MP, Manyam GC, Broom BM, Calin GA. FuncPEP v2.0: An Updated Database of Functional Short Peptides Translated from Non-Coding RNAs. Noncoding RNA 2024; 10:20. [PMID: 38668378 PMCID: PMC11054400 DOI: 10.3390/ncrna10020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
Over the past decade, there have been reports of short novel functional peptides (less than 100 aa in length) translated from so-called non-coding RNAs (ncRNAs) that have been characterized using mass spectrometry (MS) and large-scale proteomics studies. Therefore, understanding the bivalent functions of some ncRNAs as transcripts that encode both functional RNAs and short peptides, which we named ncPEPs, will deepen our understanding of biology and disease. In 2020, we published the first database of functional peptides translated from non-coding RNAs-FuncPEP. Herein, we have performed an update including the newly published ncPEPs from the last 3 years along with the categorization of host ncRNAs. FuncPEP v2.0 contains 152 functional ncPEPs, out of which 40 are novel entries. A PubMed search from August 2020 to July 2023 incorporating specific keywords was performed and screened for publications reporting validated functional peptides derived from ncRNAs. We did not observe a significant increase in newly discovered functional ncPEPs, but a steady increase. The novel identified ncPEPs included in the database were characterized by a wide array of molecular and physiological parameters (i.e., types of host ncRNA, species distribution, chromosomal density, distribution of ncRNA length, identification methods, molecular weight, and functional distribution across humans and other species). We consider that, despite the fact that MS can now easily identify ncPEPs, there still are important limitations in proving their functionality.
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Affiliation(s)
- Swati Mohapatra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.M.); (P.R.)
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
| | - Anik Banerjee
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Paola Rausseo
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.M.); (P.R.)
- Scripps College, Claremont, CA 91711, USA
| | - Mihnea P. Dragomir
- Institute of Pathology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany;
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Berlin Institute of Health at Charité, 10117 Berlin, Germany
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.)
| | - Bradley M. Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.)
| | - George A. Calin
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.M.); (P.R.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Zabeti Touchaei A, Vahidi S. MicroRNAs as regulators of immune checkpoints in cancer immunotherapy: targeting PD-1/PD-L1 and CTLA-4 pathways. Cancer Cell Int 2024; 24:102. [PMID: 38462628 PMCID: PMC10926683 DOI: 10.1186/s12935-024-03293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024] Open
Abstract
Immunotherapy has revolutionized cancer treatment by harnessing the power of the immune system to eliminate tumors. Immune checkpoint inhibitors (ICIs) block negative regulatory signals that prevent T cells from attacking cancer cells. Two key ICIs target the PD-1/PD-L1 pathway, which includes programmed death-ligand 1 (PD-L1) and its receptor programmed death 1 (PD-1). Another ICI targets cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). While ICIs have demonstrated remarkable efficacy in various malignancies, only a subset of patients respond favorably. MicroRNAs (miRNAs), small non-coding RNAs that regulate gene expression, play a crucial role in modulating immune checkpoints, including PD-1/PD-L1 and CTLA-4. This review summarizes the latest advancements in immunotherapy, highlighting the therapeutic potential of targeting PD-1/PD-L1 and CTLA-4 immune checkpoints and the regulatory role of miRNAs in modulating these pathways. Consequently, understanding the complex interplay between miRNAs and immune checkpoints is essential for developing more effective and personalized immunotherapy strategies for cancer treatment.
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Affiliation(s)
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Lee A, Lim J, Lim JS. Emerging roles of MITF as a crucial regulator of immunity. Exp Mol Med 2024; 56:311-318. [PMID: 38351314 PMCID: PMC10907664 DOI: 10.1038/s12276-024-01175-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/15/2023] [Accepted: 12/03/2023] [Indexed: 02/19/2024] Open
Abstract
Microphthalmia-associated transcription factor (MITF), a basic helix-loop-helix leucine zipper transcription factor (bHLH-Zip), has been identified as a melanocyte-specific transcription factor and plays a critical role in melanocyte survival, differentiation, function, proliferation and pigmentation. Although numerous studies have explained the roles of MITF in melanocytes and in melanoma development, the function of MITF in the hematopoietic or immune system-beyond its function in melanin-producing cells-is not yet fully understood. However, there is convincing and increasing evidence suggesting that MITF may play multiple important roles in immune-related cells. Therefore, this review is focused on recent advances in elucidating novel functions of MITF in cancer progression and immune responses to cancer. In particular, we highlight the role of MITF as a central modulator in the regulation of immune responses, as elucidated in recent studies.
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Affiliation(s)
- Aram Lee
- Department of Biological Science and the Cellular Heterogeneity Research Center, Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Jihyun Lim
- Department of Biological Science and the Cellular Heterogeneity Research Center, Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Jong-Seok Lim
- Department of Biological Science and the Cellular Heterogeneity Research Center, Research Institute of Women's Health, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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Yuan P, Teng D, de Groot E, Li M, Trousil S, Shen CH, Roszik J, Davies MA, Gopal YV, Zheng B. Loss of AMPKα2 promotes melanoma tumor growth and brain metastasis. iScience 2023; 26:106791. [PMID: 37213225 PMCID: PMC10197146 DOI: 10.1016/j.isci.2023.106791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/02/2023] [Accepted: 04/26/2023] [Indexed: 05/23/2023] Open
Abstract
AMP-activated protein kinase (AMPK) is a critical cellular energy sensor at the interface of metabolism and cancer. However, the role of AMPK in carcinogenesis remains unclear. Here, through analysis of the TCGA melanoma dataset, we found that PRKAA2 gene that encodes the α2 subunit of AMPK is mutated in ∼9% of cutaneous melanomas, and these mutations tend to co-occur with NF1 mutations. Knockout of AMPKα2 promoted anchorage-independent growth of NF1-mutant melanoma cells, whereas ectopic expression of AMPKα2 inhibited their growth in soft agar assays. Moreover, loss of AMPKα2 accelerated tumor growth of NF1-mutant melanoma and enhanced their brain metastasis in immune-deficient mice. Our findings support that AMPKα2 serves as a tumor suppressor in NF1-mutant melanoma and suggest that AMPK could be a therapeutic target for treating melanoma brain metastasis.
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Affiliation(s)
- Ping Yuan
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Da Teng
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Evelyn de Groot
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Man Li
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Sebastian Trousil
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Che-Hung Shen
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Y.N. Vashisht Gopal
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bin Zheng
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
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Dong L, Tian X, Zhao Y, Tu H, Wong A, Yang Y. The Roles of MiRNAs (MicroRNAs) in Melanoma Immunotherapy. Int J Mol Sci 2022; 23. [PMID: 36499102 DOI: 10.3390/ijms232314775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Melanoma is the most aggressive form of skin cancer, characterized by life-threatening and rapidly spreading progression. Traditional targeted therapy can alleviate tumors by inactivating hyperactive kinases such as BRAF or MEK but inevitably encounters drug resistance. The advent of immunotherapy has revolutionized melanoma treatment and significantly improved the prognosis of melanoma patients. MicroRNAs (miRNAs) are intricately involved in innate and adaptive immunity and are implicated in melanoma immunotherapy. This systematic review describes the roles of miRNAs in regulating the functions of immune cells in skin and melanoma, as well as the involvement of miRNAs in pharmacology including the effect, resistance and immune-related adverse events of checkpoint inhibitors such as PD-1 and CTLA-4 inhibitors, which are used for treating cutaneous, uveal and mucosal melanoma. The expressions and functions of miRNAs in immunotherapy employing tumor-infiltrating lymphocytes and Toll-like receptor 9 agonists are also discussed. The prospect of innovative therapeutic strategies such as the combined administration of miRNAs and immune checkpoint inhibitors and the nanotechnology-based delivery of miRNAs are also provided. A comprehensive understanding of the interplay between miRNAs and immunotherapy is crucial for the discovery of reliable biomarkers and for the development of novel miRNA-based therapeutics against melanoma.
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Zhang Y, Goto Y, Yagishita S, Shinno Y, Mizuno K, Watanabe N, Yamamoto Y, Ota N, Ochiya T, Fujita Y. Machine learning-based exceptional response prediction of nivolumab monotherapy with circulating microRNAs in non-small cell lung cancer. Lung Cancer 2022; 173:107-15. [DOI: 10.1016/j.lungcan.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022]
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Zhang X, Deng Y, Liang X, Rao Y, Zheng H, Liu F, Luo X, Yang J, Chen J, Sun D. miR-100-5p Is a Novel Biomarker That Suppresses the Proliferation, Migration, and Invasion in Skin Cutaneous Melanoma. Stem Cells Int 2022; 2022:3585540. [PMID: 36193251 PMCID: PMC9526548 DOI: 10.1155/2022/3585540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
Objective To better understand the role and underlying mechanisms of SKCM, we conducted bioinformatics analysis and in vivo experiments. Results We found its role as a tumor suppressor gene in SKCM and its effect on prognosis. In addition, this study found that miR-100-5p had a bidirectional effect on SKCM microenvironment. After exploring the relationship between the two, it was found that tumors with intermediate miR-100-5p expression had the highest level of immune cell infiltration. In addition, the value of miR-100-5p was assessed by survival analysis, univariate Cox regression analysis, and nomogram prognostic prediction. Finally, we constructed a regulatory network to illustrate the regulatory relationship of miR-100-5p. Conclusions In conclusion, the antitumor effect of miR-100-5p is revealed, and the present study is followed by a discussion of its molecular regulatory network, followed by novel insights into SKCM therapy.
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Affiliation(s)
- Xiao Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yuqi Deng
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xiao Liang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yamin Rao
- Department of Pathology, Shanghai Ninth People's Hospital, Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200011, China
| | - Haiyan Zheng
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Fei Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xusong Luo
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jun Yang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jun Chen
- Department of Dermatology, Shanghai Ninth People's Hospital, Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200011, China
| | - Di Sun
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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Levati L, Bassi C, Mastroeni S, Lupini L, Antonini Cappellini GC, Bonmassar L, Alvino E, Caporali S, Lacal PM, Narducci MG, Molineris I, De Galitiis F, Negrini M, Russo G, D’Atri S. Circulating miR-1246 and miR-485-3p as Promising Biomarkers of Clinical Response and Outcome in Melanoma Patients Treated with Targeted Therapy. Cancers (Basel) 2022; 14:cancers14153706. [PMID: 35954369 PMCID: PMC9367338 DOI: 10.3390/cancers14153706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/16/2022] [Accepted: 07/24/2022] [Indexed: 01/27/2023] Open
Abstract
Despite the significant improvements in advanced melanoma therapy, there is still a pressing need for biomarkers that can predict patient response and prognosis, and therefore support rational treatment decisions. Here, we investigated whether circulating miRNAs could be biomarkers of clinical outcomes in patients treated with targeted therapy. Using next-generation sequencing, we profiled plasma miRNAs at baseline and at progression in patients treated with BRAF inhibitors (BRAFi) or BRAFi + MEKi. Selected miRNAs associated with response to therapy were subjected to validation by real-time quantitative RT-PCR . Receiver Operating Characteristics (ROC), Kaplan–Meier and univariate and multivariate Cox regression analyses were performed on the validated miR-1246 and miR-485-3p baseline levels. The median baseline levels of miR-1246 and miR-485-3p were significantly higher and lower, respectively, in the group of patients not responding to therapy (NRs) as compared with the group of responding patients (Rs). In Rs, a trend toward an increase in miR-1246 and a decrease in miR-485-3p was observed at progression. Baseline miR-1246 level and the miR-1246/miR-485-3p ratio showed a good ability to discriminate between Rs and NRs. Poorer PFS and OS were observed in patients with unfavorable levels of at least one miRNA. In multivariate analysis, a low level of miR-485-3p and a high miR-1246/miR-485-3p ratio remained independent negative prognostic factors for PFS, while a high miR-1246/miR-485-3p ratio was associated with an increased risk of mortality, although statistical significance was not reached. Evaluation of miR-1246 and miR-485-3p baseline plasma levels might help clinicians to identify melanoma patients most likely to be unresponsive to targeted therapy or at higher risk for short-term PFS and mortality, thus improving their management.
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Affiliation(s)
- Lauretta Levati
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (L.L.); (L.B.); (S.C.); (P.M.L.); (M.G.N.); (G.R.)
| | - Cristian Bassi
- Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (C.B.); (L.L.); (M.N.)
- LTTA Center, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy
| | - Simona Mastroeni
- Clinical Epidemiology Unit, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy;
| | - Laura Lupini
- Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (C.B.); (L.L.); (M.N.)
| | - Gian Carlo Antonini Cappellini
- Department of Oncology and Dermatological Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (G.C.A.C.); (F.D.G.)
| | - Laura Bonmassar
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (L.L.); (L.B.); (S.C.); (P.M.L.); (M.G.N.); (G.R.)
| | - Ester Alvino
- Institute of Translational Pharmacology, National Council of Research, Via Fosso del Cavaliere 100, 00133 Rome, Italy;
| | - Simona Caporali
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (L.L.); (L.B.); (S.C.); (P.M.L.); (M.G.N.); (G.R.)
| | - Pedro Miguel Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (L.L.); (L.B.); (S.C.); (P.M.L.); (M.G.N.); (G.R.)
| | - Maria Grazia Narducci
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (L.L.); (L.B.); (S.C.); (P.M.L.); (M.G.N.); (G.R.)
| | - Ivan Molineris
- Department of Life Science and System Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy;
| | - Federica De Galitiis
- Department of Oncology and Dermatological Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (G.C.A.C.); (F.D.G.)
| | - Massimo Negrini
- Department of Translational Medicine, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy; (C.B.); (L.L.); (M.N.)
- LTTA Center, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy
| | - Giandomenico Russo
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (L.L.); (L.B.); (S.C.); (P.M.L.); (M.G.N.); (G.R.)
| | - Stefania D’Atri
- Laboratory of Molecular Oncology, IDI-IRCCS, Via dei Monti di Creta 104, 00167 Rome, Italy; (L.L.); (L.B.); (S.C.); (P.M.L.); (M.G.N.); (G.R.)
- Correspondence:
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